Highways4
Several authors
Created: 12-04-2024. Last modified: 20-05-2024.
Let us set some global options for all code chunks in this document.
knitr::opts_chunk$set(
message = FALSE, # Disable messages printed by R code chunks
warning = FALSE, # Disable warnings printed by R code chunks
echo = TRUE, # Show R code within code chunks in output
include = TRUE, # Include both R code and its results in output
eval = TRUE, # Evaluate R code chunks
cache = FALSE, # Enable caching of R code chunks for faster rendering
fig.align = "center",
out.width = "100%",
retina = 2,
error = TRUE,
collapse = TRUE
)
rm(list = ls())
set.seed(1982)1 Preprocessing
Let us now load some required libraries.
# Load required libraries
# inla.upgrade(testing = TRUE)
# remotes::install_github("inlabru-org/inlabru", ref = "devel")
# remotes::install_github("davidbolin/rspde", ref = "devel")
# remotes::install_github("davidbolin/metricgraph", ref = "devel")
# remotes::install_github("davidbolin/ngme2", ref = "devel")
library(INLA)
#inla.setOption(num.threads = 7)
library(inlabru)
library(rSPDE)
library(MetricGraph)
library(ngme2)
library(plotly)
library(dplyr)
library(sf)
library(here)Function standarize() below is later used to standardize
the covariate SpeedLimit.
To keep track of the changes, we provide summaries of every new created object. Those summaries can be accessed by pressing the Show buttons below
We load the graph object sf_graph (which only contains
weights) and the data (already graph-processed).
timeallprocedure <- Sys.time()
load(here("Graph_objects/graph_construction_19MAY24_FRC0134.RData"))
load(here("Data_files/data_day7142128_hour13_with_no_consecutive_zeros_19MAY24_FRC0134_graph_processed.RData"))
data_on_graph = data_on_graph %>%
dplyr::select(-datetime)We check the units of the graph.
sf_graph$get_edge_lengths() %>% head() %>% capture.output() %>% grep("^Units:", ., value = TRUE)
## [1] "Units: [km]"summary(sf_graph)
## A metric graph object with:
##
## Vertices:
## Total: 8781
## Degree 1: 15; Degree 2: 6409; Degree 3: 343; Degree 4: 1842; Degree 5: 58;
## Degree 6: 111; Degree 7: 2; Degree 8: 1;
## With incompatible directions: 0
##
## Edges:
## Total: 11104
## Lengths:
## Min: 0.00283468 ; Max: 1.480513 ; Total: 505.6148
## Weights:
## Columns: Length FRC SpeedLimit StreetName harmonicAverageSpeed medianSpeed averageSpeed sampleSize averageTravelTime medianTravelTime travelTimeRatio List_Number 5percentile 10percentile 15percentile 20percentile 25percentile 30percentile 35percentile 40percentile 45percentile 50percentile 55percentile 60percentile 65percentile 70percentile 75percentile 80percentile 85percentile 90percentile 95percentile road_type class_4 class_0 class_3 class_1 upto1 upto3 upto4 density density_per_hour
## That are circles: 0
##
## Graph units:
## Vertices unit: degrees ; Lengths unit: km
##
## Longitude and Latitude coordinates: TRUE
## Which spatial package: sf
## CRS: EPSG:4326
##
## Some characteristics of the graph:
## Connected: TRUE
## Has loops: FALSE
## Has multiple edges: TRUE
## Is a tree: FALSE
## Distance consistent: FALSE
## Has Euclidean edges: FALSE
##
## Computed quantities inside the graph:
## Laplacian: FALSE ; Geodesic distances: TRUE
## Resistance distances: FALSE ; Finite element matrices: FALSE
##
## Mesh: The graph has no mesh!
##
## Data: The graph has no data!
##
## Tolerances:
## vertex-vertex: 0.001
## vertex-edge: 0.001
## edge-edge: 0
summary(data_on_graph)
## ID speed day .distance_to_graph
## Min. :5701 Min. : 0.000 Min. :1.00 Min. :0.000000
## 1st Qu.:6592 1st Qu.: 1.609 1st Qu.:2.00 1st Qu.:0.001832
## Median :6712 Median : 17.703 Median :3.00 Median :0.004032
## Mean :7378 Mean : 20.107 Mean :2.55 Mean :0.004937
## 3rd Qu.:8739 3rd Qu.: 30.577 3rd Qu.:4.00 3rd Qu.:0.006952
## Max. :8969 Max. :114.263 Max. :4.00 Max. :0.019993
## .edge_number .distance_on_edge .group .coord_x
## Min. : 1 Min. :0.0000 Length:75899 Min. :-122.5
## 1st Qu.: 2347 1st Qu.:0.2586 Class :character 1st Qu.:-122.4
## Median : 4733 Median :0.5133 Mode :character Median :-122.4
## Mean : 4968 Mean :0.5067 Mean :-122.4
## 3rd Qu.: 7639 3rd Qu.:0.7609 3rd Qu.:-122.4
## Max. :11104 Max. :1.0000 Max. :-122.4
## .coord_y
## Min. :37.70
## 1st Qu.:37.74
## Median :37.77
## Mean :37.76
## 3rd Qu.:37.78
## Max. :37.81The following commands remove zero speed observations that are 1m away from the graph, and after that, they remove any speed observations that are 3m away from the graph.
to_remove = data_on_graph %>%
filter(speed == 0, .distance_to_graph > 0.001)
data_on_graph = setdiff(data_on_graph, to_remove) %>%
filter(.distance_to_graph <= 0.003)summary(to_remove)
## ID speed day .distance_to_graph .edge_number
## Min. :5701 Min. :0 Min. :1.000 Min. :0.001000 Min. : 1
## 1st Qu.:6588 1st Qu.:0 1st Qu.:2.000 1st Qu.:0.003133 1st Qu.: 2390
## Median :6702 Median :0 Median :3.000 Median :0.005536 Median : 4646
## Mean :7312 Mean :0 Mean :2.556 Mean :0.006552 Mean : 4912
## 3rd Qu.:8713 3rd Qu.:0 3rd Qu.:4.000 3rd Qu.:0.008880 3rd Qu.: 7550
## Max. :8969 Max. :0 Max. :4.000 Max. :0.019988 Max. :11096
## .distance_on_edge .group .coord_x .coord_y
## Min. :0.0000 Length:15402 Min. :-122.5 Min. :37.70
## 1st Qu.:0.2888 Class :character 1st Qu.:-122.4 1st Qu.:37.74
## Median :0.5322 Mode :character Median :-122.4 Median :37.77
## Mean :0.5156 Mean :-122.4 Mean :37.76
## 3rd Qu.:0.7568 3rd Qu.:-122.4 3rd Qu.:37.78
## Max. :1.0000 Max. :-122.4 Max. :37.81
summary(data_on_graph)
## ID speed day .distance_to_graph
## Min. :5701 Min. : 0.00 Min. :1.000 Min. :0.0000000
## 1st Qu.:6589 1st Qu.: 12.87 1st Qu.:2.000 1st Qu.:0.0005897
## Median :6728 Median : 24.14 Median :3.000 Median :0.0012698
## Mean :7485 Mean : 25.98 Mean :2.542 Mean :0.0013554
## 3rd Qu.:8769 3rd Qu.: 35.41 3rd Qu.:4.000 3rd Qu.:0.0020959
## Max. :8969 Max. :114.26 Max. :4.000 Max. :0.0029999
## .edge_number .distance_on_edge .group .coord_x
## Min. : 1 Min. :0.0000 Length:25843 Min. :-122.5
## 1st Qu.: 2078 1st Qu.:0.2631 Class :character 1st Qu.:-122.5
## Median : 4558 Median :0.5218 Mode :character Median :-122.4
## Mean : 4839 Mean :0.5137 Mean :-122.4
## 3rd Qu.: 7548 3rd Qu.:0.7700 3rd Qu.:-122.4
## Max. :11104 Max. :0.9998 Max. :-122.4
## .coord_y
## Min. :37.70
## 1st Qu.:37.74
## Median :37.76
## Mean :37.76
## 3rd Qu.:37.78
## Max. :37.81We add data to the graph.
sf_graph$get_data()
## # A tibble: 25,842 × 9
## ID speed day .distance_to_graph .coord_x .coord_y .edge_number
## <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 8969 99.8 1 0.000426 -122. 37.7 2
## 2 6588 91.7 1 0.00206 -122. 37.7 2
## 3 8848 99.8 1 0.00256 -122. 37.7 2
## 4 6677 14.5 1 0.000436 -122. 37.8 3
## 5 6532 16.1 1 0.00226 -122. 37.8 3
## 6 6686 25.7 1 0.000499 -122. 37.8 3
## 7 6570 17.7 1 0.00252 -122. 37.8 5
## 8 6677 29.0 1 0.00222 -122. 37.8 6
## 9 6657 24.1 1 0.00203 -122. 37.8 6
## 10 6576 17.7 1 0.000274 -122. 37.8 6
## # ℹ 25,832 more rows
## # ℹ 2 more variables: .distance_on_edge <dbl>, .group <chr>
summary(sf_graph)
## A metric graph object with:
##
## Vertices:
## Total: 8781
## Degree 1: 15; Degree 2: 6409; Degree 3: 343; Degree 4: 1842; Degree 5: 58;
## Degree 6: 111; Degree 7: 2; Degree 8: 1;
## With incompatible directions: 0
##
## Edges:
## Total: 11104
## Lengths:
## Min: 0.00283468 ; Max: 1.480513 ; Total: 505.6148
## Weights:
## Columns: Length FRC SpeedLimit StreetName harmonicAverageSpeed medianSpeed averageSpeed sampleSize averageTravelTime medianTravelTime travelTimeRatio List_Number 5percentile 10percentile 15percentile 20percentile 25percentile 30percentile 35percentile 40percentile 45percentile 50percentile 55percentile 60percentile 65percentile 70percentile 75percentile 80percentile 85percentile 90percentile 95percentile road_type class_4 class_0 class_3 class_1 upto1 upto3 upto4 density density_per_hour
## That are circles: 0
##
## Graph units:
## Vertices unit: degrees ; Lengths unit: km
##
## Longitude and Latitude coordinates: TRUE
## Which spatial package: sf
## CRS: EPSG:4326
##
## Some characteristics of the graph:
## Connected: TRUE
## Has loops: FALSE
## Has multiple edges: TRUE
## Is a tree: FALSE
## Distance consistent: FALSE
## Has Euclidean edges: FALSE
##
## Computed quantities inside the graph:
## Laplacian: FALSE ; Geodesic distances: TRUE
## Resistance distances: FALSE ; Finite element matrices: FALSE
##
## Mesh: The graph has no mesh!
##
## Data:
## Columns: ID speed day
## Groups: .group
##
## Tolerances:
## vertex-vertex: 0.001
## vertex-edge: 0.001
## edge-edge: 0We get the values of the weights at data locations. This essentially gives us covariates from the weights.
sf_graph$get_data()
## # A tibble: 101,616 × 50
## ID speed day .distance_to_graph Length FRC SpeedLimit StreetName
## <int> <dbl> <dbl> <dbl> <dbl> <chr> <dbl> <chr>
## 1 NA NA NA NA 0.0826 4 40 16th St
## 2 NA NA NA NA 0.0826 4 40 16th St
## 3 NA NA NA NA 0.0826 4 40 16th St
## 4 NA NA NA NA 0.0826 4 40 16th St
## 5 8969 99.8 1 0.000426 0.137 0 105 I-280 N
## 6 6588 91.7 1 0.00206 0.137 0 105 I-280 N
## 7 8848 99.8 1 0.00256 0.137 0 105 I-280 N
## 8 NA NA NA NA 0.137 0 105 I-280 N
## 9 NA NA NA NA 0.137 0 105 I-280 N
## 10 NA NA NA NA 0.137 0 105 I-280 N
## # ℹ 101,606 more rows
## # ℹ 42 more variables: harmonicAverageSpeed <dbl>, medianSpeed <dbl>,
## # averageSpeed <dbl>, sampleSize <int>, averageTravelTime <dbl>,
## # medianTravelTime <dbl>, travelTimeRatio <dbl>, List_Number <int>,
## # `5percentile` <int>, `10percentile` <int>, `15percentile` <int>,
## # `20percentile` <int>, `25percentile` <int>, `30percentile` <int>,
## # `35percentile` <int>, `40percentile` <int>, `45percentile` <int>, …
summary(sf_graph)
## A metric graph object with:
##
## Vertices:
## Total: 8781
## Degree 1: 15; Degree 2: 6409; Degree 3: 343; Degree 4: 1842; Degree 5: 58;
## Degree 6: 111; Degree 7: 2; Degree 8: 1;
## With incompatible directions: 0
##
## Edges:
## Total: 11104
## Lengths:
## Min: 0.00283468 ; Max: 1.480513 ; Total: 505.6148
## Weights:
## Columns: Length FRC SpeedLimit StreetName harmonicAverageSpeed medianSpeed averageSpeed sampleSize averageTravelTime medianTravelTime travelTimeRatio List_Number 5percentile 10percentile 15percentile 20percentile 25percentile 30percentile 35percentile 40percentile 45percentile 50percentile 55percentile 60percentile 65percentile 70percentile 75percentile 80percentile 85percentile 90percentile 95percentile road_type class_4 class_0 class_3 class_1 upto1 upto3 upto4 density density_per_hour
## That are circles: 0
##
## Graph units:
## Vertices unit: degrees ; Lengths unit: km
##
## Longitude and Latitude coordinates: TRUE
## Which spatial package: sf
## CRS: EPSG:4326
##
## Some characteristics of the graph:
## Connected: TRUE
## Has loops: FALSE
## Has multiple edges: TRUE
## Is a tree: FALSE
## Distance consistent: FALSE
## Has Euclidean edges: FALSE
##
## Computed quantities inside the graph:
## Laplacian: FALSE ; Geodesic distances: TRUE
## Resistance distances: FALSE ; Finite element matrices: FALSE
##
## Mesh: The graph has no mesh!
##
## Data:
## Columns: ID speed day Length FRC SpeedLimit StreetName harmonicAverageSpeed medianSpeed averageSpeed sampleSize averageTravelTime medianTravelTime travelTimeRatio List_Number 5percentile 10percentile 15percentile 20percentile 25percentile 30percentile 35percentile 40percentile 45percentile 50percentile 55percentile 60percentile 65percentile 70percentile 75percentile 80percentile 85percentile 90percentile 95percentile road_type class_4 class_0 class_3 class_1 upto1 upto3 upto4 density density_per_hour
## Groups: .group
##
## Tolerances:
## vertex-vertex: 0.001
## vertex-edge: 0.001
## edge-edge: 0When running
sf_graph$edgeweight_to_data(data_loc = TRUE), some
NA values are created (because the data is grouped). We
remove them below. We also standardize the SpeedLimit
covariate.
data = sf_graph$get_data() %>%
drop_na(-StreetName) %>% # this drops all rows with at least one NA value but without taking into account StreetName
mutate(across(c("SpeedLimit"), ~standardize(.))) %>%
dplyr::select(speed, SpeedLimit)The code of chunk below was executed only one time.
{r, eval = FALSE}
aux = data |>
rename(distance_on_edge = .distance_on_edge, edge_number = .edge_number) |>
as.data.frame() |>
dplyr::select(edge_number, distance_on_edge, .group)
distmatrixlist = list()
for (i in 1:4) {
distmatrixlist[[i]] = sf_graph$compute_geodist_PtE(PtE = aux %>%
filter(.group == as.character(i)) %>%
dplyr::select(-.group),
normalized = TRUE,
include_vertices = FALSE)
}
save(distmatrixlist, file = here("Models_output/distmatrixfixed_19May24.RData"))The code of chunk above was executed only one time.
summary(data)
## speed SpeedLimit .group .edge_number
## Min. : 0.00 Min. :-2.0263 Length:25842 Min. : 1
## 1st Qu.: 12.87 1st Qu.:-0.4784 Class :character 1st Qu.: 2078
## Median : 24.14 Median :-0.4784 Mode :character Median : 4558
## Mean : 25.98 Mean : 0.0000 Mean : 4839
## 3rd Qu.: 35.41 3rd Qu.: 0.0844 3rd Qu.: 7548
## Max. :114.26 Max. : 4.0947 Max. :11104
## .distance_on_edge .coord_x .coord_y
## Min. :0.0000 Min. :-122.5 Min. :37.70
## 1st Qu.:0.2631 1st Qu.:-122.5 1st Qu.:37.74
## Median :0.5218 Median :-122.4 Median :37.76
## Mean :0.5137 Mean :-122.4 Mean :37.76
## 3rd Qu.:0.7700 3rd Qu.:-122.4 3rd Qu.:37.78
## Max. :0.9998 Max. :-122.4 Max. :37.81We add the data again but now with the new standardized
SpeedLimit covariate.
sf_graph$get_data()
## # A tibble: 25,842 × 7
## speed SpeedLimit .coord_x .coord_y .edge_number .distance_on_edge .group
## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <chr>
## 1 99.8 4.09 -122. 37.7 2 0.195 1
## 2 91.7 4.09 -122. 37.7 2 0.227 1
## 3 99.8 4.09 -122. 37.7 2 0.363 1
## 4 14.5 -1.04 -122. 37.8 3 0.309 1
## 5 16.1 -1.04 -122. 37.8 3 0.583 1
## 6 25.7 -1.04 -122. 37.8 3 0.925 1
## 7 17.7 -1.04 -122. 37.8 5 0.0567 1
## 8 29.0 -1.04 -122. 37.8 6 0.129 1
## 9 24.1 -1.04 -122. 37.8 6 0.612 1
## 10 17.7 -1.04 -122. 37.8 6 0.755 1
## # ℹ 25,832 more rows
summary(sf_graph)
## A metric graph object with:
##
## Vertices:
## Total: 8781
## Degree 1: 15; Degree 2: 6409; Degree 3: 343; Degree 4: 1842; Degree 5: 58;
## Degree 6: 111; Degree 7: 2; Degree 8: 1;
## With incompatible directions: 0
##
## Edges:
## Total: 11104
## Lengths:
## Min: 0.00283468 ; Max: 1.480513 ; Total: 505.6148
## Weights:
## Columns: Length FRC SpeedLimit StreetName harmonicAverageSpeed medianSpeed averageSpeed sampleSize averageTravelTime medianTravelTime travelTimeRatio List_Number 5percentile 10percentile 15percentile 20percentile 25percentile 30percentile 35percentile 40percentile 45percentile 50percentile 55percentile 60percentile 65percentile 70percentile 75percentile 80percentile 85percentile 90percentile 95percentile road_type class_4 class_0 class_3 class_1 upto1 upto3 upto4 density density_per_hour
## That are circles: 0
##
## Graph units:
## Vertices unit: degrees ; Lengths unit: km
##
## Longitude and Latitude coordinates: TRUE
## Which spatial package: sf
## CRS: EPSG:4326
##
## Some characteristics of the graph:
## Connected: TRUE
## Has loops: FALSE
## Has multiple edges: TRUE
## Is a tree: FALSE
## Distance consistent: FALSE
## Has Euclidean edges: FALSE
##
## Computed quantities inside the graph:
## Laplacian: FALSE ; Geodesic distances: TRUE
## Resistance distances: FALSE ; Finite element matrices: FALSE
##
## Mesh: The graph has no mesh!
##
## Data:
## Columns: speed SpeedLimit
## Groups: .group
##
## Tolerances:
## vertex-vertex: 0.001
## vertex-edge: 0.001
## edge-edge: 0We build a mesh.
summary(sf_graph)
## A metric graph object with:
##
## Vertices:
## Total: 8781
## Degree 1: 15; Degree 2: 6409; Degree 3: 343; Degree 4: 1842; Degree 5: 58;
## Degree 6: 111; Degree 7: 2; Degree 8: 1;
## With incompatible directions: 0
##
## Edges:
## Total: 11104
## Lengths:
## Min: 0.00283468 ; Max: 1.480513 ; Total: 505.6148
## Weights:
## Columns: Length FRC SpeedLimit StreetName harmonicAverageSpeed medianSpeed averageSpeed sampleSize averageTravelTime medianTravelTime travelTimeRatio List_Number 5percentile 10percentile 15percentile 20percentile 25percentile 30percentile 35percentile 40percentile 45percentile 50percentile 55percentile 60percentile 65percentile 70percentile 75percentile 80percentile 85percentile 90percentile 95percentile road_type class_4 class_0 class_3 class_1 upto1 upto3 upto4 density density_per_hour
## That are circles: 0
##
## Graph units:
## Vertices unit: degrees ; Lengths unit: km
##
## Longitude and Latitude coordinates: TRUE
## Which spatial package: sf
## CRS: EPSG:4326
##
## Some characteristics of the graph:
## Connected: TRUE
## Has loops: FALSE
## Has multiple edges: TRUE
## Is a tree: FALSE
## Distance consistent: FALSE
## Has Euclidean edges: FALSE
##
## Computed quantities inside the graph:
## Laplacian: FALSE ; Geodesic distances: TRUE
## Resistance distances: FALSE ; Finite element matrices: FALSE
##
## Mesh:
## Max h_e: 0.04999869 ; Min n_e: 0
##
## Data:
## Columns: speed SpeedLimit
## Groups: .group
##
## Tolerances:
## vertex-vertex: 0.001
## vertex-edge: 0.001
## edge-edge: 0We get the value of the weights at mesh locations. This will allow us
to built matrices B.sigma and B.range below.
Again,
sf_graph$edgeweight_to_data(mesh = TRUE, add = FALSE, return = TRUE)
creates repeated information (because the data is grouped). We fix that
by filtering one group. We also standardize the SpeedLimit
covariate.
mesh = sf_graph$edgeweight_to_data(mesh = TRUE,
add = FALSE,
return = TRUE) %>%
filter(.group == 1) %>%
mutate(across(c("SpeedLimit"), ~standardize(.))) %>%
dplyr:::select.data.frame(SpeedLimit)summary(mesh)
## SpeedLimit
## Min. :-1.91072
## 1st Qu.:-0.76409
## Median :-0.34714
## Mean : 0.00000
## 3rd Qu.: 0.06981
## Max. : 2.623661.1 Stationary model
- Observe that we are considering replicates.
stat.time.ini <- Sys.time()
################################################################################
################################# STATIONARY MODEL #############################
################################################################################
rspde_model_stat <- rspde.metric_graph(sf_graph,
parameterization = "matern",
nu.upper.bound = 1.5)str(rspde_model_stat)
## List of 20
## $ f :List of 3
## ..$ model : chr "cgeneric"
## ..$ n : int 41796
## ..$ cgeneric:List of 5
## .. ..$ model: chr "inla_cgeneric_rspde_stat_general_model"
## .. ..$ shlib: chr "/home/rierasl/R/x86_64-pc-linux-gnu-library/4.4/INLA/bin/linux/64bit/external/rSPDE/librSPDE.so"
## .. ..$ n : int 41796
## .. ..$ debug: logi FALSE
## .. ..$ data :List of 5
## .. .. ..$ ints :List of 5
## .. .. .. ..$ n : int 41796
## .. .. .. ..$ debug : int 0
## .. .. .. ..$ graph_opt_i: int [1:186659] 0 0 0 0 0 0 0 0 0 1 ...
## .. .. .. ..$ graph_opt_j: int [1:186659] 0 1 805 5399 5681 8781 11429 11463 13882 1 ...
## .. .. .. ..$ rspde.order: int 2
## .. .. ..$ doubles :List of 11
## .. .. .. ..$ d : num 1
## .. .. .. ..$ nu.upper.bound : num 1.5
## .. .. .. ..$ matrices_less : num [1:143229] 0.0534 0 0 0 0 ...
## .. .. .. ..$ matrices_full : num [1:277832] 0.0534 0 0 0 0 ...
## .. .. .. ..$ start.theta : num [1:2] 0 1.35
## .. .. .. ..$ theta.prior.mean : num [1:2] 0 1.35
## .. .. .. ..$ prior.nu.loglocation: num -0.288
## .. .. .. ..$ prior.nu.mean : num 0.75
## .. .. .. ..$ prior.nu.prec : num 3
## .. .. .. ..$ prior.nu.logscale : num 1
## .. .. .. ..$ start.nu : num 0.75
## .. .. ..$ characters:List of 5
## .. .. .. ..$ model : chr "inla_cgeneric_rspde_stat_general_model"
## .. .. .. ..$ shlib : chr "/home/rierasl/R/x86_64-pc-linux-gnu-library/4.4/INLA/bin/linux/64bit/external/rSPDE/librSPDE.so"
## .. .. .. ..$ prior.nu.dist : chr "lognormal"
## .. .. .. ..$ parameterization : chr "matern"
## .. .. .. ..$ prior.theta.param: chr "theta"
## .. .. ..$ matrices :List of 2
## .. .. .. ..$ rational_table : num [1:5996] 999 6 0.001 0.412 0.005 ...
## .. .. .. ..$ theta.prior.prec: num [1:6] 2 2 0.1 0 0 0.1
## .. .. ..$ smatrices : list()
## .. ..- attr(*, "class")= chr "inla.cgeneric"
## $ cgeneric_type : chr "general"
## $ theta.prior.mean : num [1:2] 0 1.35
## $ prior.nu :List of 4
## ..$ loglocation: num -0.288
## ..$ mean : num 0.75
## ..$ prec : num 3
## ..$ logscale : num 1
## $ theta.prior.prec : num [1:2, 1:2] 0.1 0 0 0.1
## $ start.nu : num 0.75
## $ integer.nu : logi FALSE
## $ start.theta : num [1:2] 0 1.35
## $ stationary : logi TRUE
## $ rspde.order : num 2
## $ dim : num 1
## $ est_nu : logi TRUE
## $ nu.upper.bound : num 1.5
## $ prior.nu.dist : chr "lognormal"
## $ debug : logi FALSE
## $ type.rational.approx: chr "chebfun"
## $ mesh :Classes 'metric_graph', 'R6' <metric_graph>
## Public:
## add_mesh_observations: function (data = NULL, group = NULL)
## add_observations: function (data = NULL, edge_number = "edge_number", distance_on_edge = "distance_on_edge",
## build_mesh: function (h = NULL, n = NULL, continuous = TRUE, continuous.outs = FALSE,
## buildC: function (alpha = 2, edge_constraint = FALSE)
## buildDirectionalConstraints: function (alpha = 1)
## C: NULL
## characteristics: list
## check_distance_consistency: function ()
## check_euclidean: function ()
## clear_observations: function ()
## clone: function (deep = FALSE)
## CoB: NULL
## compute_characteristics: function (check_euclidean = FALSE)
## compute_fem: function (petrov = FALSE)
## compute_geodist: function (full = FALSE, obs = TRUE, group = NULL, verbose = 0)
## compute_geodist_mesh: function ()
## compute_geodist_PtE: function (PtE, normalized = TRUE, include_vertices = TRUE, verbose = 0)
## compute_laplacian: function (full = FALSE, obs = TRUE, group = NULL, verbose = 0)
## compute_PtE_edges: function ()
## compute_resdist: function (full = FALSE, obs = TRUE, group = NULL, check_euclidean = FALSE,
## compute_resdist_mesh: function ()
## compute_resdist_PtE: function (PtE, normalized = TRUE, include_vertices = FALSE, check_euclidean = FALSE,
## coordinates: function (PtE = NULL, XY = NULL, normalized = TRUE)
## drop_na: function (...)
## E: 1 3 5 7 9 9 10 12 13 14 15 12 18 19 21 20 22 24 26 28 30 ...
## edge_lengths: 0.0820202978316493 0.13610246403764 0.07378151878521 0.0 ...
## edges: metric_graph_edges
## edgeweight_to_data: function (loc = NULL, mesh = FALSE, data_loc = FALSE, weight_col = NULL,
## fem_basis: function (PtE)
## filter: function (..., .drop_na = FALSE, .drop_all_na = TRUE)
## geo_dist: list
## get_data: function (group = NULL, tibble = TRUE, drop_na = FALSE, drop_all_na = TRUE)
## get_degrees: function (which = "degree")
## get_edge_lengths: function (unit = NULL)
## get_edge_weights: function (data.frame = FALSE, tibble = TRUE)
## get_groups: function (get_cols = FALSE)
## get_initial_graph: function ()
## get_locations: function ()
## get_mesh_locations: function (bru = FALSE, loc = NULL, normalized = TRUE)
## get_PtE: function ()
## get_vertices_incomp_dir: function ()
## initialize: function (edges = NULL, V = NULL, E = NULL, vertex_unit = NULL,
## is_tree: function ()
## Laplacian: NULL
## mesh: list
## mesh_A: function (PtE)
## mutate: function (..., .drop_na = FALSE, .drop_all_na = TRUE)
## nE: 11104
## nV: 8781
## observation_to_vertex: function (tolerance = 1e-15, mesh_warning = TRUE)
## plot: function (data = NULL, newdata = NULL, group = 1, plotly = FALSE,
## plot_connections: function ()
## plot_function: function (data = NULL, newdata = NULL, group = 1, X = NULL, plotly = FALSE,
## plot_movie: function (X, plotly = TRUE, vertex_size = 5, vertex_color = "black",
## print: function ()
## process_data: function (data = NULL, edge_number = "edge_number", distance_on_edge = "distance_on_edge",
## prune_vertices: function (check_weights = TRUE, verbose = FALSE)
## PtV: NULL
## res_dist: NULL
## select: function (..., .drop_na = FALSE, .drop_all_na = TRUE)
## set_edge_weights: function (weights = rep(1, self$nE), kirchhoff_weights = NULL)
## summarise: function (..., .include_graph_groups = FALSE, .groups = NULL,
## summary: function (messages = FALSE, compute_characteristics = TRUE, check_euclidean = TRUE,
## V: -122.40171 -122.40078 -122.44449 -122.44331 -122.41216 - ...
## vertices: metric_graph_vertices
## VtEfirst: function ()
## Private:
## A: function (group = NULL, obs_to_vert = FALSE, drop_na = FALSE,
## add_vertices: function (PtE, tolerance = 1e-10, verbose)
## addinfo: FALSE
## clear_initial_info: function ()
## compute_degrees: function ()
## compute_laplacian_PtE: function (PtE, normalized = TRUE, verbose = verbose)
## compute_lengths: function (longlat, unit, crs, proj4string, which_longlat, vertex_unit,
## connected: TRUE
## coordinates_multiple_snaps: function (XY, tolerance, verbose = verbose, crs, proj4string,
## create_update_vertices: function ()
## crs: crs
## data: metric_graph_data, list
## edge_weights: tbl_df, tbl, data.frame
## find_edge_edge_points: function (tol, verbose, crs, proj4string, longlat, fact, which_longlat)
## find_mesh_bc: function ()
## get_edge_weights_internal: function (data.frame = FALSE)
## group_col: .group
## initial_edges_added: NULL
## initial_graph: metric_graph, R6
## kirchhoff_weights: NULL
## length_unit: km
## line_to_vertex: function (tolerance = 0, longlat = FALSE, fact, verbose, crs,
## longlat: TRUE
## merge_close_vertices: function (tolerance, fact)
## merge.all.deg2: function ()
## mesh_merge_deg2: function ()
## mesh_merge_outs: function ()
## move_V_first: function ()
## plot_2d: function (line_width = 0.1, marker_size = 1, vertex_color = "black",
## plot_3d: function (line_width = 1, marker_size = 1, vertex_color = "rgb(0,0,0)",
## proj4string: NULL
## prune_warning: FALSE
## pruned: FALSE
## PtE_to_mesh: function (PtE)
## ref_edges: 1 5502 2 359 3 4077 4 5117 5 7 5419 8 9 10 11 4817 4613 ...
## remove_circles: function (threshold, verbose, longlat, unit, crs, proj4string,
## remove.first.deg2: function (res)
## set_first_weights: function (weights = rep(1, self$nE))
## set_petrov_matrices: function ()
## split_edge: function (Ei, t, tolerance = 0)
## temp_PtE: NULL
## tolerance: list
## transform: FALSE
## vertex_unit: degrees
## which_longlat: sf
## $ fem_mesh :List of 5
## ..$ c0:Formal class 'dgTMatrix' [package "Matrix"] with 6 slots
## .. .. ..@ i : int [1:13932] 0 1 2 3 4 5 6 7 8 9 ...
## .. .. ..@ j : int [1:13932] 0 1 2 3 4 5 6 7 8 9 ...
## .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. ..@ Dimnames:List of 2
## .. .. .. ..$ : NULL
## .. .. .. ..$ : NULL
## .. .. ..@ x : num [1:13932] 0.0534 0.0776 0.0408 0.0457 0.0367 ...
## .. .. ..@ factors : list()
## ..$ g1:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. ..@ i : int [1:44204] 0 5681 8781 11463 1 8781 11429 11463 13882 2 ...
## .. .. ..@ p : int [1:13933] 0 4 9 12 15 18 23 26 29 34 ...
## .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. ..@ Dimnames:List of 2
## .. .. .. ..$ : NULL
## .. .. .. ..$ : NULL
## .. .. ..@ x : num [1:44204] 210.6 -161.9 -24.4 -24.4 103.4 ...
## .. .. ..@ factors : list()
## ..$ g2:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. ..@ i : int [1:81554] 0 1 5399 5681 8781 11463 0 1 4450 8781 ...
## .. .. ..@ p : int [1:13933] 0 6 13 18 23 28 37 42 47 56 ...
## .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. ..@ Dimnames:List of 2
## .. .. .. ..$ : NULL
## .. .. .. ..$ : NULL
## .. .. ..@ x : num [1:81554] 1731368 28997 607384 -2117274 -125237 ...
## .. .. ..@ factors : list()
## ..$ g3:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. ..@ i : int [1:124984] 0 1 805 5399 5681 8781 11429 11463 13882 0 ...
## .. .. ..@ p : int [1:13933] 0 9 18 25 32 43 56 65 72 85 ...
## .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. ..@ Dimnames:List of 2
## .. .. .. ..$ : NULL
## .. .. .. ..$ : NULL
## .. .. ..@ x : num [1:124984] 1.84e+10 1.88e+08 -4.79e+08 9.57e+09 -2.57e+10 ...
## .. .. ..@ factors : list()
## ..$ g4:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. ..@ i : int [1:175232] 0 1 804 805 4450 5399 5681 8781 11429 11463 ...
## .. .. ..@ p : int [1:13933] 0 11 23 32 41 58 76 89 98 116 ...
## .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. ..@ Dimnames:List of 2
## .. .. .. ..$ : NULL
## .. .. .. ..$ : NULL
## .. .. ..@ x : num [1:175232] 2.12e+14 1.39e+12 8.54e+11 -8.78e+12 1.53e+10 ...
## .. .. ..@ factors : list()
## $ parameterization : chr "matern"
## $ n.spde : int 13932
## - attr(*, "class")= chr [1:3] "rspde_metric_graph" "inla_rspde" "inla.cgeneric"str(data_rspde_bru_stat)
## List of 4
## $ data :List of 8
## ..$ speed : num [1:25842] 99.8 91.7 99.8 14.5 16.1 ...
## ..$ SpeedLimit : num [1:25842] 4.09 4.09 4.09 -1.04 -1.04 ...
## ..$ .coord_x : num [1:25842] -122 -122 -122 -122 -122 ...
## ..$ .coord_y : num [1:25842] 37.7 37.7 37.7 37.8 37.8 ...
## ..$ .edge_number : num [1:25842] 2 2 2 3 3 3 5 6 6 6 ...
## ..$ .distance_on_edge: num [1:25842] 0.195 0.227 0.363 0.309 0.583 ...
## ..$ .group : chr [1:25842] "1" "1" "1" "1" ...
## ..$ loc : num [1:25842, 1:2] 2 2 2 3 3 3 5 6 6 6 ...
## ..- attr(*, "class")= chr [1:2] "metric_graph_data" "list"
## $ index:List of 3
## ..$ field : int [1:55728] 1 2 3 4 5 6 7 8 9 10 ...
## ..$ field.group: int [1:55728] 1 1 1 1 1 1 1 1 1 1 ...
## ..$ field.repl : int [1:55728] 1 1 1 1 1 1 1 1 1 1 ...
## ..- attr(*, "class")= chr [1:2] "inla_rspde_index" "list"
## ..- attr(*, "rspde.order")= num 0
## ..- attr(*, "integer_nu")= logi TRUE
## ..- attr(*, "n.mesh")= int 13932
## ..- attr(*, "name")= chr "field"
## ..- attr(*, "n.group")= int 1
## ..- attr(*, "n.repl")= int 4
## $ repl : chr [1:25842] "1" "1" "1" "1" ...
## $ basis:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. ..@ i : int [1:155052] 0 1 3 8 9 10 11 12 13 14 ...
## .. ..@ p : int [1:167185] 0 0 0 2 2 10 16 16 16 21 ...
## .. ..@ Dim : int [1:2] 25842 167184
## .. ..@ Dimnames:List of 2
## .. .. ..$ : NULL
## .. .. ..$ : NULL
## .. ..@ x : num [1:155052] 0.416 0.319 0.382 0.224 0.509 ...
## .. ..@ factors : list()cmp_stat = speed ~ -1 +
Intercept(1) +
SpeedLimit +
field(loc, model = rspde_model_stat,
replicate = data_rspde_bru_stat[["repl"]])
rspde_fit_stat <-
bru(cmp_stat,
data = data_rspde_bru_stat[["data"]],
family = "T",
options = list(verbose = FALSE)
)str(rspde_fit_stat)
## List of 56
## $ names.fixed : chr [1:2] "Intercept" "SpeedLimit"
## $ summary.fixed :'data.frame': 2 obs. of 7 variables:
## ..$ mean : num [1:2] 23.6 8.07
## ..$ sd : num [1:2] 0.0918 0.1543
## ..$ 0.025quant: num [1:2] 23.42 7.77
## ..$ 0.5quant : num [1:2] 23.6 8.07
## ..$ 0.975quant: num [1:2] 23.78 8.37
## ..$ mode : num [1:2] 23.6 8.07
## ..$ kld : num [1:2] 0 0
## $ marginals.fixed :List of 2
## ..$ Intercept : num [1:43, 1:2] 23.2 23.3 23.3 23.4 23.4 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : NULL
## .. .. ..$ : chr [1:2] "x" "y"
## ..$ SpeedLimit: num [1:43, 1:2] 7.41 7.5 7.59 7.71 7.77 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : NULL
## .. .. ..$ : chr [1:2] "x" "y"
## $ summary.lincomb :'data.frame': 0 obs. of 0 variables
## $ marginals.lincomb : NULL
## $ size.lincomb : NULL
## $ summary.lincomb.derived :'data.frame': 0 obs. of 0 variables
## $ marginals.lincomb.derived : NULL
## $ size.lincomb.derived : NULL
## $ mlik : num [1:2, 1] -191638 -191633
## ..- attr(*, "dimnames")=List of 2
## .. ..$ : chr [1:2] "log marginal-likelihood (integration)" "log marginal-likelihood (Gaussian)"
## .. ..$ : NULL
## $ cpo :List of 3
## ..$ cpo : logi(0)
## ..$ pit : logi(0)
## ..$ failure: logi(0)
## $ gcpo :List of 5
## ..$ gcpo : NULL
## ..$ kld : NULL
## ..$ mean : NULL
## ..$ sd : NULL
## ..$ groups: NULL
## $ po :List of 1
## ..$ po: num [1:25842] 0.000686 0.001311 0.000709 0.044981 0.044299 ...
## $ waic :List of 4
## ..$ waic : num 219620
## ..$ p.eff : num 2089
## ..$ local.waic : num [1:25842] 14.65 13.41 14.63 6.22 6.26 ...
## ..$ local.p.eff: num [1:25842] 0.04249 0.06627 0.06233 0.00678 0.01083 ...
## $ residuals :List of 1
## ..$ deviance.residuals: num [1:25842] 2.919 0 2.911 0 -0.396 ...
## $ model.random : chr "CGeneric"
## $ summary.random :List of 1
## ..$ field:'data.frame': 167184 obs. of 8 variables:
## .. ..$ ID : num [1:167184] 1 2 3 4 5 6 7 8 9 10 ...
## .. ..$ mean : num [1:167184] -0.005432 -0.000555 0.599316 0.087342 -0.428828 ...
## .. ..$ sd : num [1:167184] 1.54 1.76 2.2 2.25 1.96 ...
## .. ..$ 0.025quant: num [1:167184] -3.02 -3.46 -3.72 -4.32 -4.27 ...
## .. ..$ 0.5quant : num [1:167184] -0.005432 -0.000555 0.599316 0.087342 -0.428828 ...
## .. ..$ 0.975quant: num [1:167184] 3.01 3.46 4.92 4.5 3.41 ...
## .. ..$ mode : num [1:167184] -0.005432 -0.000555 0.599316 0.087342 -0.428828 ...
## .. ..$ kld : num [1:167184] 0 0 0 0 0 0 0 0 0 0 ...
## $ marginals.random :List of 1
## ..$ field:List of 167184
## .. ..$ index.1 : num [1:43, 1:2] -6.56 -5.72 -4.75 -3.58 -3.02 ...
## .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. ..$ : NULL
## .. .. .. ..$ : chr [1:2] "x" "y"
## .. ..$ index.2 : num [1:43, 1:2] -7.52 -6.56 -5.45 -4.1 -3.46 ...
## .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. ..$ : NULL
## .. .. .. ..$ : chr [1:2] "x" "y"
## .. ..$ index.3 : num [1:43, 1:2] -8.8 -7.59 -6.21 -4.53 -3.72 ...
## .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. ..$ : NULL
## .. .. .. ..$ : chr [1:2] "x" "y"
## .. ..$ index.4 : num [1:43, 1:2] -9.51 -8.28 -6.87 -5.15 -4.32 ...
## .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. ..$ : NULL
## .. .. .. ..$ : chr [1:2] "x" "y"
## .. ..$ index.5 : num [1:43, 1:2] -8.78 -7.71 -6.48 -4.99 -4.27 ...
## .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. ..$ : NULL
## .. .. .. ..$ : chr [1:2] "x" "y"
## .. ..$ index.6 : num [1:43, 1:2] -5.98 -5.07 -4.02 -2.74 -2.12 ...
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## .. .. .. ..$ : chr [1:2] "x" "y"
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## .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. ..$ : NULL
## .. .. .. ..$ : chr [1:2] "x" "y"
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## .. .. .. ..$ : NULL
## .. .. .. ..$ : chr [1:2] "x" "y"
## .. ..$ index.9 : num [1:43, 1:2] -7.06 -6.17 -5.15 -3.91 -3.32 ...
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## .. .. .. ..$ : NULL
## .. .. .. ..$ : chr [1:2] "x" "y"
## .. ..$ index.10 : num [1:43, 1:2] -9.58 -8.52 -7.3 -5.82 -5.11 ...
## .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. ..$ : NULL
## .. .. .. ..$ : chr [1:2] "x" "y"
## .. ..$ index.11 : num [1:43, 1:2] -9.53 -8.4 -7.1 -5.52 -4.76 ...
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## .. .. .. ..$ : chr [1:2] "x" "y"
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## .. .. .. ..$ : chr [1:2] "x" "y"
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## .. .. .. ..$ : chr [1:2] "x" "y"
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## .. .. .. ..$ : chr [1:2] "x" "y"
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## .. .. .. ..$ : chr [1:2] "x" "y"
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## .. .. .. ..$ : chr [1:2] "x" "y"
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## .. .. .. ..$ : chr [1:2] "x" "y"
## .. ..$ index.21 : num [1:43, 1:2] -6.59 -5.8 -4.88 -3.77 -3.24 ...
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## .. .. .. ..$ : chr [1:2] "x" "y"
## .. ..$ index.22 : num [1:43, 1:2] -7.35 -6.42 -5.36 -4.06 -3.44 ...
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## .. ..$ index.24 : num [1:43, 1:2] -7.53 -6.62 -5.58 -4.31 -3.7 ...
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## .. .. .. ..$ : chr [1:2] "x" "y"
## .. ..$ index.25 : num [1:43, 1:2] -6.2 -5.36 -4.39 -3.22 -2.65 ...
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## .. ..$ index.26 : num [1:43, 1:2] -8.61 -7.4 -6.02 -4.34 -3.53 ...
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## .. .. .. ..$ : chr [1:2] "x" "y"
## .. ..$ index.27 : num [1:43, 1:2] -4.265 -3.369 -2.336 -1.081 -0.479 ...
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## .. ..$ index.28 : num [1:43, 1:2] -9.82 -8.7 -7.41 -5.84 -5.09 ...
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## .. .. .. ..$ : chr [1:2] "x" "y"
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## .. .. .. ..$ : chr [1:2] "x" "y"
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## .. .. .. ..$ : chr [1:2] "x" "y"
## .. ..$ index.34 : num [1:43, 1:2] -9.36 -8.16 -6.78 -5.11 -4.3 ...
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## .. .. .. ..$ : chr [1:2] "x" "y"
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## .. .. .. ..$ : chr [1:2] "x" "y"
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## .. .. .. ..$ : chr [1:2] "x" "y"
## .. ..$ index.37 : num [1:43, 1:2] -8.67 -7.57 -6.3 -4.77 -4.03 ...
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## .. .. .. ..$ : chr [1:2] "x" "y"
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## .. ..$ N : num 41796
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## ..$ kld : num [1:193028] 0 0 0 0 0 0 0 0 0 0 ...
## $ marginals.linear.predictor : NULL
## $ summary.fitted.values :'data.frame': 193028 obs. of 6 variables:
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## ..$ sd : num [1:193028] 2.9 3.01 3.49 2.17 2.53 ...
## ..$ 0.025quant: num [1:193028] 52.8 52.7 51.9 10.7 11.2 ...
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## ..$ 0.975quant: num [1:193028] 64.2 64.5 65.6 19.2 21.1 ...
## ..$ mode : num [1:193028] 58.5 58.6 58.8 15 16.1 ...
## $ marginals.fitted.values : NULL
## $ size.linear.predictor :List of 5
## ..$ n : num 167186
## ..$ N : num 167186
## ..$ Ntotal: num 193028
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## $ summary.hyperpar :'data.frame': 5 obs. of 6 variables:
## ..$ mean : num [1:5] 0.00103 2.12123 3.08696 -0.00194 -0.88777
## ..$ sd : num [1:5] 1.76e-07 2.87e-05 4.33e-04 2.24e-04 1.78e-04
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## ..$ mode : num [1:5] 0.00103 2.12122 3.08735 -0.00204 -0.88771
## $ marginals.hyperpar :List of 5
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## .. ..- attr(*, "dimnames")=List of 2
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## ..$ Theta1 for field : num [1:43, 1:2] 3.08 3.08 3.09 3.09 3.09 ...
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## $ internal.summary.hyperpar :'data.frame': 5 obs. of 6 variables:
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## ..$ sd : num [1:5] 0.000171 0.000236 0.000432 0.000224 0.000178
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## ..$ mode : num [1:5] -6.88167 -2.11013 3.08735 -0.00203 -0.88771
## $ internal.marginals.hyperpar:List of 5
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## .. ..- attr(*, "dimnames")=List of 2
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## .. .. ..$ : chr [1:2] "x" "y"
## ..$ dof_intern for student-t : num [1:43, 1:2] -2.11 -2.11 -2.11 -2.11 -2.11 ...
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## ..$ Theta1 for field : num [1:43, 1:2] 3.08 3.08 3.09 3.09 3.09 ...
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## $ offset.linear.predictor : num [1:193028] 0 0 0 0 0 0 0 0 0 0 ...
## $ model.spde2.blc : NULL
## $ summary.spde2.blc : list()
## $ marginals.spde2.blc : NULL
## $ size.spde2.blc : NULL
## $ model.spde3.blc : NULL
## $ summary.spde3.blc : list()
## $ marginals.spde3.blc : NULL
## $ size.spde3.blc : NULL
## $ logfile : chr [1:2873] "[PANUA] PARDISO License is expired." "[PANUA] Please obtain a new PARDISO license at https://www.panua.ch/products/pardiso" " Read ntt 24 1 with max.threads 24" " Found num.threads = 24:1 max_threads = 24" ...
## $ misc :List of 22
## ..$ cov.intern : num [1:5, 1:5] 4.41e-08 7.94e-09 1.85e-08 -2.61e-09 -2.24e-09 ...
## ..$ cor.intern : num [1:5, 1:5] 1 0.1555 0.286 -0.0569 -0.0568 ...
## ..$ cov.intern.eigenvalues : num [1:5] 2.91e-08 3.16e-08 1.03e-07 5.04e-08 6.65e-08
## ..$ cov.intern.eigenvectors : num [1:5, 1:5] 0.654 -0.457 -0.286 0.501 -0.177 ...
## ..$ reordering : int [1:167186] 138940 138946 161633 161595 137173 137136 137028 136820 137176 136912 ...
## ..$ theta.tags : chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## ..$ log.posterior.mode : num -191596
## ..$ stdev.corr.negative : num [1:5] 0.634 1.458 0.44 1.421 0.646
## ..$ stdev.corr.positive : num [1:5] 1.576 0.686 2.272 0.704 1.548
## ..$ to.theta :List of 5
## .. ..$ log precision for the student-t observations:function (x)
## .. ..$ dof_intern for student-t :function (x)
## .. ..$ Theta1 for field :function (x)
## .. ..$ Theta2 for field :function (x)
## .. ..$ Theta3 for field :function (x)
## ..$ from.theta :List of 5
## .. ..$ log precision for the student-t observations:function (x)
## .. ..$ dof_intern for student-t :function (x)
## .. ..$ Theta1 for field :function (x)
## .. ..$ Theta2 for field :function (x)
## .. ..$ Theta3 for field :function (x)
## ..$ mode.status : num 0
## ..$ lincomb.derived.correlation.matrix: NULL
## ..$ lincomb.derived.covariance.matrix : NULL
## ..$ opt.directions : num [1:5, 1:5] -0.177 0.487 0.361 -0.389 0.67 ...
## .. ..- attr(*, "dimnames")=List of 2
## .. .. ..$ : chr [1:5] "theta:1" "theta:2" "theta:3" "theta:4" ...
## .. .. ..$ : chr [1:5] "dir:1" "dir:2" "dir:3" "dir:4" ...
## ..$ configs :List of 17
## .. ..$ .preopt : logi TRUE
## .. ..$ lite : logi FALSE
## .. ..$ mpred : int 25842
## .. ..$ npred : int 167186
## .. ..$ mnpred : int 193028
## .. ..$ Npred : int 25842
## .. ..$ n : int 167186
## .. ..$ nz : int 994610
## .. ..$ prior_nz : int 746638
## .. ..$ ntheta : int 5
## .. ..$ nconfig : int 27
## .. ..$ offsets : num [1:193028] 0 0 0 0 0 0 0 0 0 0 ...
## .. ..$ contents :List of 3
## .. .. ..$ tag : chr [1:5] "APredictor" "Predictor" "field" "Intercept" ...
## .. .. ..$ start : int [1:5] 1 25843 193029 360213 360214
## .. .. ..$ length: int [1:5] 25842 167186 167184 1 1
## .. ..$ A :Formal class 'dgTMatrix' [package "Matrix"] with 6 slots
## .. .. .. ..@ i : int [1:167186] 2 3 4 5 6 7 8 9 10 11 ...
## .. .. .. ..@ j : int [1:167186] 0 1 2 3 4 5 6 7 8 9 ...
## .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. ..$ : NULL
## .. .. .. .. ..$ : NULL
## .. .. .. ..@ x : num [1:167186] 1 1 1 1 1 1 1 1 1 1 ...
## .. .. .. ..@ factors : list()
## .. ..$ pA :Formal class 'dgTMatrix' [package "Matrix"] with 6 slots
## .. .. .. ..@ i : int [1:206658] 0 1 2 3 4 5 6 7 8 9 ...
## .. .. .. ..@ j : int [1:206658] 0 0 0 0 0 0 0 0 0 0 ...
## .. .. .. ..@ Dim : int [1:2] 25842 167186
## .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. ..$ : NULL
## .. .. .. .. ..$ : NULL
## .. .. .. ..@ x : num [1:206658] 1 1 1 1 1 1 1 1 1 1 ...
## .. .. .. ..@ factors : list()
## .. ..$ config :List of 27
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88166 -2.11014 3.08738 -0.00205 -0.8877
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -110
## .. .. .. ..$ log.posterior.orig: num -105
## .. .. .. ..$ mean : num [1:167186] -0.005432 -0.000555 0.599316 0.087342 -0.428828 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005432 -0.000555 0.599316 0.087342 -0.428828 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.549 0 0.273 0.13 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.36 0.241 3.11 4.854 0.097 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.549 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.070707 0.085051 0.071123 -0.012421 -0.000656 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.597285 8.069441 -0.005432 -0.000555 0.599316 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88123 -2.11045 3.08719 -0.00172 -0.88782
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -91.5
## .. .. .. ..$ log.posterior.orig: num -88.2
## .. .. .. ..$ mean : num [1:167186] -0.005441 -0.000556 0.599223 0.087386 -0.428779 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005441 -0.000556 0.599223 0.087386 -0.428779 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.55 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.3591 0.2412 3.1081 4.8525 0.0971 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.55 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.070703 0.085047 0.071119 -0.012444 -0.000672 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.596987 8.068551 -0.005441 -0.000556 0.599223 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88184 -2.11002 3.08745 -0.00218 -0.88766
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -115
## .. .. .. ..$ log.posterior.orig: num -112
## .. .. .. ..$ mean : num [1:167186] -0.005429 -0.000555 0.599353 0.087324 -0.428848 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005429 -0.000555 0.599353 0.087324 -0.428848 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.549 0 0.273 0.13 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.3608 0.2412 3.1101 4.8548 0.0969 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.549 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.07071 0.08505 0.07112 -0.01241 -0.00065 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.597404 8.069798 -0.005429 -0.000555 0.599353 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.8816 -2.1101 3.0873 -0.0021 -0.8874
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -114
## .. .. .. ..$ log.posterior.orig: num -111
## .. .. .. ..$ mean : num [1:167186] -0.005431 -0.000555 0.599323 0.08733 -0.428899 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005431 -0.000555 0.599323 0.08733 -0.428899 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.549 0 0.273 0.13 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.361 0.241 3.11 4.854 0.097 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.549 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.070706 0.08505 0.071122 -0.012422 -0.000659 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.59717 8.069262 -0.005431 -0.000555 0.599323 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88188 -2.11019 3.08749 -0.00194 -0.88828
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -96.9
## .. .. .. ..$ log.posterior.orig: num -93.7
## .. .. .. ..$ mean : num [1:167186] -0.005435 -0.000556 0.599301 0.087368 -0.428677 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005435 -0.000556 0.599301 0.087368 -0.428677 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.55 0 0.273 0.13 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.36 0.241 3.109 4.853 0.097 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.55 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.07071 0.08505 0.07112 -0.01242 -0.00065 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.597528 8.069818 -0.005435 -0.000556 0.599301 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88214 -2.1099 3.08569 -0.00223 -0.8879
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -3.27
## .. .. .. ..$ log.posterior.orig: num 0
## .. .. .. ..$ mean : num [1:167186] -0.005458 -0.000559 0.599089 0.087546 -0.427705 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005458 -0.000559 0.599089 0.087546 -0.427705 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.551 0 0.274 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.3554 0.2414 3.1035 4.847 0.0973 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.551 0 0.274 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.070718 0.085065 0.071133 -0.012423 -0.000626 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.598828 8.071503 -0.005458 -0.000559 0.599089 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88157 -2.11019 3.0877 -0.00201 -0.88766
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -129
## .. .. .. ..$ log.posterior.orig: num -126
## .. .. .. ..$ mean : num [1:167186] -0.005427 -0.000554 0.59936 0.087302 -0.429046 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005427 -0.000554 0.59936 0.087302 -0.429046 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.549 0 0.273 0.13 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.3612 0.2412 3.1107 4.8555 0.0969 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.549 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.070705 0.085049 0.071121 -0.012421 -0.000662 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.596985 8.069042 -0.005427 -0.000554 0.59936 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88145 -2.1101 3.08737 -0.00234 -0.88784
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -113
## .. .. .. ..$ log.posterior.orig: num -110
## .. .. .. ..$ mean : num [1:167186] -0.005431 -0.000555 0.599316 0.08733 -0.428913 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005431 -0.000555 0.599316 0.08733 -0.428913 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.549 0 0.273 0.13 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.361 0.241 3.11 4.854 0.097 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.549 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.070705 0.08505 0.071122 -0.012424 -0.000661 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.597117 8.069144 -0.005431 -0.000555 0.599316 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88209 -2.11024 3.08739 -0.00147 -0.88742
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -98.3
## .. .. .. ..$ log.posterior.orig: num -95
## .. .. .. ..$ mean : num [1:167186] -0.005434 -0.000555 0.599316 0.087366 -0.428657 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005434 -0.000555 0.599316 0.087366 -0.428657 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.55 0 0.273 0.13 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.36 0.241 3.109 4.854 0.097 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.55 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.070709 0.085054 0.071125 -0.012415 -0.000647 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.597623 8.070039 -0.005434 -0.000555 0.599316 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88139 -2.10929 3.08739 -0.00166 -0.88779
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -92.9
## .. .. .. ..$ log.posterior.orig: num -89.7
## .. .. .. ..$ mean : num [1:167186] -0.005435 -0.000556 0.599336 0.087378 -0.428571 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005435 -0.000556 0.599336 0.087378 -0.428571 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.55 0 0.273 0.13 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.36 0.241 3.109 4.853 0.097 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.55 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.07071 0.08506 0.07113 -0.01241 -0.00064 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.597808 8.070422 -0.005435 -0.000556 0.599336 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88178 -2.1105 3.08737 -0.00221 -0.88767
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -115
## .. .. .. ..$ log.posterior.orig: num -112
## .. .. .. ..$ mean : num [1:167186] -0.005431 -0.000555 0.599307 0.087327 -0.428935 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005431 -0.000555 0.599307 0.087327 -0.428935 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.549 0 0.273 0.13 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.3606 0.2412 3.1099 4.8545 0.0969 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.549 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.070704 0.085048 0.07112 -0.012426 -0.000663 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.597066 8.069032 -0.005431 -0.000555 0.599307 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88187 -2.10979 3.08762 -0.00161 -0.88783
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -104
## .. .. .. ..$ log.posterior.orig: num -101
## .. .. .. ..$ mean : num [1:167186] -0.005432 -0.000555 0.599355 0.087355 -0.428675 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005432 -0.000555 0.599355 0.087355 -0.428675 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.55 0 0.273 0.13 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.36 0.241 3.109 4.854 0.097 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.55 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.070711 0.085056 0.071128 -0.012408 -0.000642 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.597699 8.0703 -0.005432 -0.000555 0.599355 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88175 -2.11027 3.0876 -0.00224 -0.88797
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -121
## .. .. .. ..$ log.posterior.orig: num -117
## .. .. .. ..$ mean : num [1:167186] -0.005429 -0.000555 0.599341 0.087316 -0.428953 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005429 -0.000555 0.599341 0.087316 -0.428953 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.549 0 0.273 0.13 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.3609 0.2412 3.1103 4.855 0.0969 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.549 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.070705 0.08505 0.071122 -0.012419 -0.000658 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.59714 8.069274 -0.005429 -0.000555 0.599341 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.8823 -2.1102 3.08671 -0.00195 -0.88788
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -57.7
## .. .. .. ..$ log.posterior.orig: num -54.4
## .. .. .. ..$ mean : num [1:167186] -0.005444 -0.000557 0.599221 0.087441 -0.428238 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005444 -0.000557 0.599221 0.087441 -0.428238 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.55 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.358 0.2413 3.1067 4.8508 0.0971 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.55 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.070713 0.085059 0.071129 -0.012416 -0.000636 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.598191 8.070777 -0.005444 -0.000557 0.599221 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88183 -2.1096 3.08671 -0.00209 -0.88813
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -54.6
## .. .. .. ..$ log.posterior.orig: num -51.3
## .. .. .. ..$ mean : num [1:167186] -0.005444 -0.000557 0.599233 0.087447 -0.428191 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005444 -0.000557 0.599233 0.087447 -0.428191 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.55 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.3579 0.2413 3.1066 4.8506 0.0971 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.55 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.070715 0.085062 0.071131 -0.012413 -0.000632 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.598293 8.070993 -0.005444 -0.000557 0.599233 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.8819 -2.11031 3.08754 -0.00193 -0.8874
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -121
## .. .. .. ..$ log.posterior.orig: num -118
## .. .. .. ..$ mean : num [1:167186] -0.005428 -0.000554 0.599351 0.087315 -0.428939 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005428 -0.000554 0.599351 0.087315 -0.428939 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.549 0 0.273 0.13 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.361 0.2412 3.1104 4.8551 0.0969 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.549 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.070706 0.08505 0.071122 -0.012417 -0.000656 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.597203 8.069418 -0.005428 -0.000554 0.599351 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88143 -2.1097 3.08754 -0.00207 -0.88765
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -118
## .. .. .. ..$ log.posterior.orig: num -115
## .. .. .. ..$ mean : num [1:167186] -0.005428 -0.000555 0.599364 0.087321 -0.42889 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005428 -0.000555 0.599364 0.087321 -0.42889 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.549 0 0.273 0.13 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.3609 0.2412 3.1102 4.8549 0.0969 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.549 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.070708 0.085053 0.071125 -0.012414 -0.000652 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.597308 8.069641 -0.005428 -0.000555 0.599364 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88198 -2.10963 3.08664 -0.00178 -0.88756
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -55.4
## .. .. .. ..$ log.posterior.orig: num -52.1
## .. .. .. ..$ mean : num [1:167186] -0.005443 -0.000557 0.599243 0.087447 -0.428176 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005443 -0.000557 0.599243 0.087447 -0.428176 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.55 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.358 0.2413 3.1067 4.8507 0.0971 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.55 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.07072 0.08506 0.07113 -0.01241 -0.00063 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.598359 8.071144 -0.005443 -0.000557 0.599243 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88186 -2.11011 3.08663 -0.00242 -0.8877
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -71.9
## .. .. .. ..$ log.posterior.orig: num -68.7
## .. .. .. ..$ mean : num [1:167186] -0.00544 -0.000556 0.59923 0.087407 -0.428452 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.00544 -0.000556 0.59923 0.087407 -0.428452 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.55 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.3586 0.2413 3.1075 4.8517 0.0971 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.55 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.07071 0.085056 0.071126 -0.012422 -0.000646 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.597803 8.070126 -0.00544 -0.000556 0.59923 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88177 -2.11052 3.08749 -0.00165 -0.88785
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -103
## .. .. .. ..$ log.posterior.orig: num -99.9
## .. .. .. ..$ mean : num [1:167186] -0.005436 -0.000556 0.599283 0.08736 -0.428808 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005436 -0.000556 0.599283 0.08736 -0.428808 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.55 0 0.273 0.13 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.36 0.241 3.109 4.854 0.097 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.55 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.070704 0.085049 0.071121 -0.012429 -0.000662 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.597178 8.069115 -0.005436 -0.000556 0.599283 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88131 -2.10992 3.08749 -0.00179 -0.8881
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -100
## .. .. .. ..$ log.posterior.orig: num -96.9
## .. .. .. ..$ mean : num [1:167186] -0.005436 -0.000556 0.599296 0.087367 -0.42876 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005436 -0.000556 0.599296 0.087367 -0.42876 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.55 0 0.273 0.13 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.36 0.241 3.109 4.853 0.097 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.55 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.070707 0.085052 0.071123 -0.012427 -0.000658 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.597283 8.069333 -0.005436 -0.000556 0.599296 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.8819 -2.1099 3.0866 -0.0015 -0.888
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -37.3
## .. .. .. ..$ log.posterior.orig: num -34
## .. .. .. ..$ mean : num [1:167186] -0.005451 -0.000558 0.599175 0.087492 -0.428045 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005451 -0.000558 0.599175 0.087492 -0.428045 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.551 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.3569 0.2413 3.1054 4.8492 0.0972 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.551 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.070714 0.085061 0.07113 -0.012423 -0.000636 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.598333 8.070836 -0.005451 -0.000558 0.599175 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88174 -2.11032 3.08658 -0.00214 -0.88815
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -53.8
## .. .. .. ..$ log.posterior.orig: num -50.5
## .. .. .. ..$ mean : num [1:167186] -0.005448 -0.000558 0.599162 0.087452 -0.428321 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005448 -0.000558 0.599162 0.087452 -0.428321 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.551 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.3576 0.2413 3.1062 4.8501 0.0972 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:746638] 0.551 0 0.273 0.131 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ cpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "skewness"
## .. .. .. ..$ gcpodens.moments : num[0 , 1:3]
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "mean" "variance" "log.theta.correction"
## .. .. .. ..$ arg.str : NULL
## .. .. .. ..$ ll.info : num [1:25842, 1:3] 0.070709 0.085054 0.071125 -0.012435 -0.000652 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:3] "gradient" "hessian" "deriv3"
## .. .. .. ..$ APredictor : num [1:25842, 1:2] 58.5 58.6 58.8 15 16.1 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. .. ..$ Predictor : num [1:167186, 1:2] 23.597778 8.069821 -0.005448 -0.000558 0.599162 ...
## .. .. .. .. ..- attr(*, "dimnames")=List of 2
## .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. .. ..$ :List of 15
## .. .. .. ..$ theta : Named num [1:5] -6.88145 -2.10996 3.08743 -0.00147 -0.88753
## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## .. .. .. ..$ log.posterior : num -101
## .. .. .. ..$ log.posterior.orig: num -97.7
## .. .. .. ..$ mean : num [1:167186] -0.005435 -0.000556 0.599306 0.087366 -0.428745 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005435 -0.000556 0.599306 0.087366 -0.428745 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
## .. .. .. ..$ Q :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 0.55 0 0.273 0.13 0 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qinv :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:994610] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
## .. .. .. .. .. ..@ Dim : int [1:2] 167186 167186
## .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. ..@ x : num [1:994610] 2.36 0.241 3.109 4.853 0.097 ...
## .. .. .. .. .. ..@ factors : list()
## .. .. .. ..$ Qprior :Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. ..@ i : int [1:746638] 0 0 1 2 2 3 4 4 5 6 ...
## .. .. .. .. .. ..@ p : int [1:167187] 0 1 3 4 6 7 9 10 12 15 ...
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## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
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## .. .. .. ..$ log.posterior.orig: num -114
## .. .. .. ..$ mean : num [1:167186] -0.005432 -0.000555 0.599292 0.087326 -0.429022 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005432 -0.000555 0.599292 0.087326 -0.429022 ...
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## .. .. .. ..$ log.posterior.orig: num -51.3
## .. .. .. ..$ mean : num [1:167186] -0.005447 -0.000558 0.599172 0.087452 -0.428307 ...
## .. .. .. ..$ improved.mean : num [1:167186] -0.005447 -0.000558 0.599172 0.087452 -0.428307 ...
## .. .. .. ..$ skewness : logi [1:167186] NA NA NA NA NA NA ...
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## .. .. .. .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
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## .. .. .. ..$ log.posterior.orig: num -48.3
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## .. .. .. ..$ improved.mean : num [1:167186] -0.005447 -0.000558 0.599184 0.087458 -0.428259 ...
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## .. .. .. .. .. ..$ : chr [1:2] "mean" "variance"
## .. ..$ max.log.posterior: num -191491
## ..$ nfunc : num 1822
## ..$ warnings : chr "Stupid local search strategy used: This is usually a sign of a ill-defined model and/or non-informative data."
## ..$ opt.trace :List of 3
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## .. .. .. ..$ : chr [1:320] "iter1" "iter2" "iter3" "iter4" ...
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## ..$ linkfunctions :List of 2
## .. ..$ names: chr "identity"
## .. ..$ link : int [1:25842] 1 1 1 1 1 1 1 1 1 1 ...
## ..$ family : int [1:25842] 1 1 1 1 1 1 1 1 1 1 ...
## $ dic :List of 14
## ..$ dic : num 218459
## ..$ p.eff : num 951
## ..$ mean.deviance : num 217508
## ..$ deviance.mean : num 216557
## ..$ dic.sat : num -7817
## ..$ mean.deviance.sat: num -8768
## ..$ deviance.mean.sat: num 3325
## ..$ family.dic : num 218459
## ..$ family.dic.sat : num -20862
## ..$ family.p.eff : num 951
## ..$ family : num [1:25842] 1 1 1 1 1 1 1 1 1 1 ...
## ..$ local.dic : num [1:25842] 14.6 13.32 14.55 6.33 6.4 ...
## ..$ local.dic.sat : num [1:25842] 8.505 -16.487 8.454 -32.801 0.314 ...
## ..$ local.p.eff : num [1:25842] -0.0152 -0.0216 -0.021 0.1176 0.1576 ...
## $ mode :List of 5
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## .. ..- attr(*, "names")= chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## ..$ x : num [1:360214] 94.9 95.4 97.2 15.2 17.9 ...
## ..$ theta.tags : chr [1:5] "log precision for the student-t observations" "dof_intern for student-t" "Theta1 for field" "Theta2 for field" ...
## ..$ mode.status : num 0
## ..$ log.posterior.mode: num -191596
## $ joint.hyper :'data.frame': 1 obs. of 7 variables:
## ..$ log precision for the student-t observations: num -6.88
## ..$ dof_intern for student-t : num -2.11
## ..$ Theta1 for field : num 3.09
## ..$ Theta2 for field : num -0.00223
## ..$ Theta3 for field : num -0.888
## ..$ Log posterior density : num -191533
## ..$ Total integration weight (log.dens included): int 1
## $ nhyper : int 5
## $ version :List of 2
## ..$ inla.call: chr "GITCOMMIT [b51fb385728e90bce98ca92b1d8762a2d13f655c - Sat May 18 13:21:08 2024 +0300]"
## ..$ R.INLA : Named chr "24.05.18-2"
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## $ Q : NULL
## $ graph : NULL
## $ ok : logi TRUE
## $ cpu.intern : chr [1:16] "Wall-clock time used on [/tmp/RtmpQjnBgO/file320ac362947e9a/Model.ini]" "Preparations : 0.389 seconds" "Approx inference (stage1): 2700.316 seconds" "Approx inference (stage2): 0.002 seconds" ...
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## .. .. ..$ prior.prec: num 0.001
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## $ .args :List of 30
## ..$ formula :Class 'formula' language BRU.response ~ f(Intercept, model = BRU_Intercept_main_model, ngroup = 1, nrep = 1, values = BRU_Intercept_v| __truncated__ ...
## ..$ family : chr "t"
## ..$ data :List of 21
## .. ..$ BRU.response : num [1:25842] 99.8 91.7 99.8 14.5 16.1 ...
## .. ..$ BRU.E : num [1:25842] 1 1 1 1 1 1 1 1 1 1 ...
## .. ..$ BRU.Ntrials : num [1:25842] 1 1 1 1 1 1 1 1 1 1 ...
## .. ..$ BRU.weights : num [1:25842] 1 1 1 1 1 1 1 1 1 1 ...
## .. ..$ BRU.scale : num [1:25842] 1 1 1 1 1 1 1 1 1 1 ...
## .. ..$ BRU.offset : num [1:25842] 0 0 0 0 0 0 0 0 0 0 ...
## .. ..$ Intercept : num [1:167186] 1 NA NA NA NA NA NA NA NA NA ...
## .. ..$ Intercept.group : int [1:167186] 1 NA NA NA NA NA NA NA NA NA ...
## .. ..$ Intercept.repl : int [1:167186] 1 NA NA NA NA NA NA NA NA NA ...
## .. ..$ SpeedLimit : num [1:167186] NA 1 NA NA NA NA NA NA NA NA ...
## .. ..$ SpeedLimit.group : int [1:167186] NA 1 NA NA NA NA NA NA NA NA ...
## .. ..$ SpeedLimit.repl : int [1:167186] NA 1 NA NA NA NA NA NA NA NA ...
## .. ..$ field : int [1:167186] NA NA 1 2 3 4 5 6 7 8 ...
## .. ..$ field.group : int [1:167186] NA NA 1 1 1 1 1 1 1 1 ...
## .. ..$ field.repl : int [1:167186] NA NA 1 1 1 1 1 1 1 1 ...
## .. ..$ BRU_Intercept_main_model : chr "linear"
## .. ..$ BRU_Intercept_values : num 1
## .. ..$ BRU_SpeedLimit_main_model: chr "linear"
## .. ..$ BRU_SpeedLimit_values : num 1
## .. ..$ BRU_field_main_model :List of 20
## .. .. ..$ f :List of 3
## .. .. .. ..$ model : chr "cgeneric"
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## .. .. .. .. ..$ model: chr "inla_cgeneric_rspde_stat_general_model"
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## .. .. .. .. .. .. ..$ rspde.order: int 2
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## .. .. .. .. .. .. ..$ nu.upper.bound : num 1.5
## .. .. .. .. .. .. ..$ matrices_less : num [1:143229] 0.0534 0 0 0 0 ...
## .. .. .. .. .. .. ..$ matrices_full : num [1:277832] 0.0534 0 0 0 0 ...
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## .. .. .. .. .. .. ..$ theta.prior.mean : num [1:2] 0 1.35
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## .. .. .. .. .. .. ..$ parameterization : chr "matern"
## .. .. .. .. .. .. ..$ prior.theta.param: chr "theta"
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## .. .. ..$ prior.nu.dist : chr "lognormal"
## .. .. ..$ debug : logi FALSE
## .. .. ..$ type.rational.approx: chr "chebfun"
## .. .. ..$ mesh :Classes 'metric_graph', 'R6' <metric_graph>
## Public:
## add_mesh_observations: function (data = NULL, group = NULL)
## add_observations: function (data = NULL, edge_number = "edge_number", distance_on_edge = "distance_on_edge",
## build_mesh: function (h = NULL, n = NULL, continuous = TRUE, continuous.outs = FALSE,
## buildC: function (alpha = 2, edge_constraint = FALSE)
## buildDirectionalConstraints: function (alpha = 1)
## C: NULL
## characteristics: list
## check_distance_consistency: function ()
## check_euclidean: function ()
## clear_observations: function ()
## clone: function (deep = FALSE)
## CoB: NULL
## compute_characteristics: function (check_euclidean = FALSE)
## compute_fem: function (petrov = FALSE)
## compute_geodist: function (full = FALSE, obs = TRUE, group = NULL, verbose = 0)
## compute_geodist_mesh: function ()
## compute_geodist_PtE: function (PtE, normalized = TRUE, include_vertices = TRUE, verbose = 0)
## compute_laplacian: function (full = FALSE, obs = TRUE, group = NULL, verbose = 0)
## compute_PtE_edges: function ()
## compute_resdist: function (full = FALSE, obs = TRUE, group = NULL, check_euclidean = FALSE,
## compute_resdist_mesh: function ()
## compute_resdist_PtE: function (PtE, normalized = TRUE, include_vertices = FALSE, check_euclidean = FALSE,
## coordinates: function (PtE = NULL, XY = NULL, normalized = TRUE)
## drop_na: function (...)
## E: 1 3 5 7 9 9 10 12 13 14 15 12 18 19 21 20 22 24 26 28 30 ...
## edge_lengths: 0.0820202978316493 0.13610246403764 0.07378151878521 0.0 ...
## edges: metric_graph_edges
## edgeweight_to_data: function (loc = NULL, mesh = FALSE, data_loc = FALSE, weight_col = NULL,
## fem_basis: function (PtE)
## filter: function (..., .drop_na = FALSE, .drop_all_na = TRUE)
## geo_dist: list
## get_data: function (group = NULL, tibble = TRUE, drop_na = FALSE, drop_all_na = TRUE)
## get_degrees: function (which = "degree")
## get_edge_lengths: function (unit = NULL)
## get_edge_weights: function (data.frame = FALSE, tibble = TRUE)
## get_groups: function (get_cols = FALSE)
## get_initial_graph: function ()
## get_locations: function ()
## get_mesh_locations: function (bru = FALSE, loc = NULL, normalized = TRUE)
## get_PtE: function ()
## get_vertices_incomp_dir: function ()
## initialize: function (edges = NULL, V = NULL, E = NULL, vertex_unit = NULL,
## is_tree: function ()
## Laplacian: NULL
## mesh: list
## mesh_A: function (PtE)
## mutate: function (..., .drop_na = FALSE, .drop_all_na = TRUE)
## nE: 11104
## nV: 8781
## observation_to_vertex: function (tolerance = 1e-15, mesh_warning = TRUE)
## plot: function (data = NULL, newdata = NULL, group = 1, plotly = FALSE,
## plot_connections: function ()
## plot_function: function (data = NULL, newdata = NULL, group = 1, X = NULL, plotly = FALSE,
## plot_movie: function (X, plotly = TRUE, vertex_size = 5, vertex_color = "black",
## print: function ()
## process_data: function (data = NULL, edge_number = "edge_number", distance_on_edge = "distance_on_edge",
## prune_vertices: function (check_weights = TRUE, verbose = FALSE)
## PtV: NULL
## res_dist: NULL
## select: function (..., .drop_na = FALSE, .drop_all_na = TRUE)
## set_edge_weights: function (weights = rep(1, self$nE), kirchhoff_weights = NULL)
## summarise: function (..., .include_graph_groups = FALSE, .groups = NULL,
## summary: function (messages = FALSE, compute_characteristics = TRUE, check_euclidean = TRUE,
## V: -122.40171 -122.40078 -122.44449 -122.44331 -122.41216 - ...
## vertices: metric_graph_vertices
## VtEfirst: function ()
## Private:
## A: function (group = NULL, obs_to_vert = FALSE, drop_na = FALSE,
## add_vertices: function (PtE, tolerance = 1e-10, verbose)
## addinfo: FALSE
## clear_initial_info: function ()
## compute_degrees: function ()
## compute_laplacian_PtE: function (PtE, normalized = TRUE, verbose = verbose)
## compute_lengths: function (longlat, unit, crs, proj4string, which_longlat, vertex_unit,
## connected: TRUE
## coordinates_multiple_snaps: function (XY, tolerance, verbose = verbose, crs, proj4string,
## create_update_vertices: function ()
## crs: crs
## data: metric_graph_data, list
## edge_weights: tbl_df, tbl, data.frame
## find_edge_edge_points: function (tol, verbose, crs, proj4string, longlat, fact, which_longlat)
## find_mesh_bc: function ()
## get_edge_weights_internal: function (data.frame = FALSE)
## group_col: .group
## initial_edges_added: NULL
## initial_graph: metric_graph, R6
## kirchhoff_weights: NULL
## length_unit: km
## line_to_vertex: function (tolerance = 0, longlat = FALSE, fact, verbose, crs,
## longlat: TRUE
## merge_close_vertices: function (tolerance, fact)
## merge.all.deg2: function ()
## mesh_merge_deg2: function ()
## mesh_merge_outs: function ()
## move_V_first: function ()
## plot_2d: function (line_width = 0.1, marker_size = 1, vertex_color = "black",
## plot_3d: function (line_width = 1, marker_size = 1, vertex_color = "rgb(0,0,0)",
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## prune_warning: FALSE
## pruned: FALSE
## PtE_to_mesh: function (PtE)
## ref_edges: 1 5502 2 359 3 4077 4 5117 5 7 5419 8 9 10 11 4817 4613 ...
## remove_circles: function (threshold, verbose, longlat, unit, crs, proj4string,
## remove.first.deg2: function (res)
## set_first_weights: function (weights = rep(1, self$nE))
## set_petrov_matrices: function ()
## split_edge: function (Ei, t, tolerance = 0)
## temp_PtE: NULL
## tolerance: list
## transform: FALSE
## vertex_unit: degrees
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## .. .. .. ..$ to.theta :function (x)
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## .. .. ..$ theta17 :List of 11
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## .. .. .. ..$ short.name : chr "b17"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[17] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[17] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. ..$ theta18 :List of 11
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## .. .. .. ..$ name : chr "beta18"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b18"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[18] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[18] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. ..$ theta19 :List of 11
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## .. .. .. ..$ name : chr "beta19"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b19"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[19] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[19] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. .. ..$ name : chr "beta20"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b20"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[20] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[20] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. ..$ theta21 :List of 11
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## .. .. .. ..$ name : chr "beta21"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b21"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[21] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[21] for lp_scale"
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. ..$ theta22 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta22"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b22"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[22] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[22] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. ..$ theta23 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta23"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b23"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[23] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[23] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. ..$ prior : chr "normal"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ param : num [1:2] 1 10
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta24 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta24"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b24"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[24] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[24] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. ..$ prior : chr "normal"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ param : num [1:2] 1 10
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta25 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta25"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b25"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[25] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[25] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ initial : num 1
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. ..$ param : num [1:2] 1 10
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta26 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta26"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b26"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[26] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[26] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ initial : num 1
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. ..$ param : num [1:2] 1 10
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta27 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta27"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b27"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[27] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[27] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta28 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta28"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b28"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[28] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[28] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ initial : num 1
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta29 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta29"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b29"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[29] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[29] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ initial : num 1
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta30 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta30"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b30"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[30] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[30] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta31 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta31"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b31"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[31] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[31] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ initial : num 1
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta32 :List of 11
## .. .. .. ..$ hyperid : num 103032
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta32"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b32"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[32] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[32] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ initial : num 1
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta33 :List of 11
## .. .. .. ..$ hyperid : num 103033
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta33"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b33"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[33] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[33] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ initial : num 1
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. ..$ param : num [1:2] 1 10
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
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## .. .. .. ..$ short.name : chr "b34"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[34] for lp_scale"
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## .. .. .. ..$ output.name.intern: chr "beta[34] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[35] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[35] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b36"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[36] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[36] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b37"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[37] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[37] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b38"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[38] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[38] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. ..$ theta39 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta39"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b39"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[39] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[39] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta40 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta40"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b40"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[40] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[40] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. ..$ to.theta :function (x)
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## .. .. ..$ theta41 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta41"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b41"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[41] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[41] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. ..$ param : num [1:2] 1 10
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta42 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta42"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b42"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[42] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[42] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta43 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta43"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b43"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[43] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[43] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta44 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta44"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b44"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[44] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[44] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta45 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta45"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b45"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[45] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[45] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta46 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta46"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b46"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[46] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[46] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta47 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta47"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b47"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[47] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[47] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. ..$ to.theta :function (x)
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta48 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta48"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b48"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[48] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[48] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ initial : num 1
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta49 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta49"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b49"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[49] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[49] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ initial : num 1
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. ..$ param : num [1:2] 1 10
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta50 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta50"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b50"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[50] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[50] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ initial : num 1
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. ..$ param : num [1:2] 1 10
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta51 :List of 11
## .. .. .. ..$ hyperid : num 103051
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta51"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b51"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[51] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[51] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ initial : num 1
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## .. .. .. ..$ output.name : chr "beta[54] for lp_scale"
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## .. .. .. ..$ output.name.intern: chr "beta[54] for lp_scale"
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[55] for lp_scale"
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## .. .. .. ..$ output.name : chr "beta[58] for lp_scale"
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## .. .. .. ..$ output.name.intern: chr "beta[58] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. .. ..$ short.name : chr "b59"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[59] for lp_scale"
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## .. .. .. ..$ output.name.intern: chr "beta[59] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b60"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[60] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[60] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[61] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[61] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[62] for lp_scale"
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## .. .. .. ..$ output.name.intern: chr "beta[62] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. .. ..$ short.name : chr "b63"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[63] for lp_scale"
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## .. .. .. ..$ output.name.intern: chr "beta[63] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. ..$ theta64 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[64] for lp_scale"
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## .. .. .. ..$ output.name.intern: chr "beta[64] for lp_scale"
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[65] for lp_scale"
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## .. .. .. ..$ output.name.intern: chr "beta[65] for lp_scale"
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[66] for lp_scale"
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## .. .. .. ..$ output.name.intern: chr "beta[66] for lp_scale"
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## .. .. .. ..$ output.name : chr "beta[67] for lp_scale"
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## .. .. .. ..$ output.name.intern: chr "beta[67] for lp_scale"
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## .. .. ..$ theta68 :List of 11
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## .. .. .. ..$ output.name : chr "beta[68] for lp_scale"
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## .. .. .. ..$ output.name.intern: chr "beta[68] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. ..$ theta69 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b69"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. ..$ to.theta :function (x)
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b71"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[71] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[71] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. .. ..$ name : chr "beta72"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b72"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[72] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[72] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. ..$ theta73 :List of 11
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## .. .. .. ..$ name : chr "beta73"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b73"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[73] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[73] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. ..$ to.theta :function (x)
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## .. .. ..$ theta74 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta74"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b74"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[74] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[74] for lp_scale"
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## .. .. .. ..$ to.theta :function (x)
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## .. .. ..$ theta75 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta75"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b75"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[75] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[75] for lp_scale"
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
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## .. .. ..$ theta76 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta76"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b76"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[76] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[76] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. ..$ prior : chr "normal"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ param : num [1:2] 1 10
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta77 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta77"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b77"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[77] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[77] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. ..$ prior : chr "normal"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ param : num [1:2] 1 10
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta78 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta78"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b78"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[78] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[78] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta79 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta79"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b79"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[79] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[79] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta80 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta80"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b80"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[80] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[80] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta81 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta81"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b81"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[81] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[81] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta82 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b82"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[82] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[82] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta83 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta83"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b83"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[83] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[83] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta84 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta84"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b84"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[84] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[84] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta85 :List of 11
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta85"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b85"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[85] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[85] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
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## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. .. ..$ from.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
## .. .. ..$ theta86 :List of 11
## .. .. .. ..$ hyperid : num 103086
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ name : chr "beta86"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ short.name : chr "b86"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name : chr "beta[86] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ output.name.intern: chr "beta[86] for lp_scale"
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ initial : num 1
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## .. .. .. ..$ prior : chr "normal"
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## .. .. .. ..$ param : num [1:2] 1 10
## .. .. .. .. ..- attr(*, "inla.read.only")= logi FALSE
## .. .. .. ..$ to.theta :function (x)
## .. .. .. .. ..- attr(*, "inla.read.only")= logi TRUE
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## .. .. ..- attr(*, "class")= chr "inla.data.stack.info"
## .. ..- attr(*, "class")= chr "inla.data.stack"
## ..$ track :'data.frame': 334378 obs. of 6 variables:
## .. ..$ effect : chr [1:334378] "Intercept" "SpeedLimit" "field" "field" ...
## .. ..$ index : num [1:334378] 1 1 1 2 3 4 5 6 7 8 ...
## .. ..$ iteration : num [1:334378] 0 0 0 0 0 0 0 0 0 0 ...
## .. ..$ mode : num [1:334378] NA NA NA NA NA NA NA NA NA NA ...
## .. ..$ sd : num [1:334378] NA NA NA NA NA NA NA NA NA NA ...
## .. ..$ new_linearisation: num [1:334378] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ timings :'data.frame': 2 obs. of 5 variables:
## .. ..$ Task : chr [1:2] "Preprocess" "Run inla()"
## .. ..$ Iteration: num [1:2] 1 1
## .. ..$ Time : 'difftime' num [1:2] 232.129 10037.928
## .. .. ..- attr(*, "units")= chr "secs"
## .. ..$ System : 'difftime' num [1:2] 2.014 1.292
## .. .. ..- attr(*, "units")= chr "secs"
## .. ..$ Elapsed : 'difftime' num [1:2] 233.046 2714.517
## .. .. ..- attr(*, "units")= chr "secs"
## $ bru_timings :'data.frame': 3 obs. of 5 variables:
## ..$ Task : chr [1:3] "Preprocess" "Preprocess" "Run inla()"
## ..$ Iteration: num [1:3] 0 1 1
## ..$ Time : 'difftime' num [1:3] 0.0579999999999998 232.129 10037.928
## .. ..- attr(*, "units")= chr "secs"
## ..$ System : 'difftime' num [1:3] 0 2.014 1.292
## .. ..- attr(*, "units")= chr "secs"
## ..$ Elapsed : 'difftime' num [1:3] 0.0579999999999998 233.046 2714.517
## .. ..- attr(*, "units")= chr "secs"
## $ bru_info :List of 6
## ..$ method : chr "bru"
## ..$ model :List of 2
## .. ..$ effects:List of 3
## .. .. ..$ Intercept :List of 12
## .. .. .. ..$ label : chr "Intercept"
## .. .. .. ..$ inla.formula:Class 'formula' language ~. + f(Intercept, model = BRU_Intercept_main_model, ngroup = 1, nrep = 1, values = BRU_Intercept_values)
## .. .. .. .. .. ..- attr(*, ".Environment")=<environment: R_GlobalEnv>
## .. .. .. ..$ main :List of 8
## .. .. .. .. ..$ input :List of 4
## .. .. .. .. .. ..$ input : num 1
## .. .. .. .. .. ..$ label : chr "Intercept"
## .. .. .. .. .. ..$ layer : NULL
## .. .. .. .. .. ..$ selector: NULL
## .. .. .. .. .. ..- attr(*, "class")= chr [1:2] "bru_input" "list"
## .. .. .. .. ..$ mapper : list()
## .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_linear" "bru_mapper" "list"
## .. .. .. .. ..$ model : chr "linear"
## .. .. .. .. ..$ type : chr "linear"
## .. .. .. .. ..$ n : int 1
## .. .. .. .. ..$ values : num 1
## .. .. .. .. ..$ season.length : NULL
## .. .. .. .. ..$ factor_mapping: NULL
## .. .. .. .. ..- attr(*, "class")= chr [1:2] "bru_subcomponent" "list"
## .. .. .. ..$ group :List of 8
## .. .. .. .. ..$ input :List of 4
## .. .. .. .. .. ..$ input : int 1
## .. .. .. .. .. ..$ label : chr "Intercept.group"
## .. .. .. .. .. ..$ layer : NULL
## .. .. .. .. .. ..$ selector: NULL
## .. .. .. .. .. ..- attr(*, "class")= chr [1:2] "bru_input" "list"
## .. .. .. .. ..$ mapper :List of 1
## .. .. .. .. .. ..$ n: num 1
## .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_index" "bru_mapper" "list"
## .. .. .. .. ..$ model : chr "exchangeable"
## .. .. .. .. ..$ type : chr "exchangeable"
## .. .. .. .. ..$ n : num 1
## .. .. .. .. ..$ values : int 1
## .. .. .. .. ..$ season.length : NULL
## .. .. .. .. ..$ factor_mapping: NULL
## .. .. .. .. ..- attr(*, "class")= chr [1:2] "bru_subcomponent" "list"
## .. .. .. ..$ replicate :List of 8
## .. .. .. .. ..$ input :List of 4
## .. .. .. .. .. ..$ input : int 1
## .. .. .. .. .. ..$ label : chr "Intercept.repl"
## .. .. .. .. .. ..$ layer : NULL
## .. .. .. .. .. ..$ selector: NULL
## .. .. .. .. .. ..- attr(*, "class")= chr [1:2] "bru_input" "list"
## .. .. .. .. ..$ mapper :List of 1
## .. .. .. .. .. ..$ n: num 1
## .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_index" "bru_mapper" "list"
## .. .. .. .. ..$ model : chr "iid"
## .. .. .. .. ..$ type : chr "iid"
## .. .. .. .. ..$ n : num 1
## .. .. .. .. ..$ values : int 1
## .. .. .. .. ..$ season.length : NULL
## .. .. .. .. ..$ factor_mapping: NULL
## .. .. .. .. ..- attr(*, "class")= chr [1:2] "bru_subcomponent" "list"
## .. .. .. ..$ weights : NULL
## .. .. .. ..$ copy : NULL
## .. .. .. ..$ marginal : NULL
## .. .. .. ..$ env :<environment: R_GlobalEnv>
## .. .. .. ..$ env_extra :<environment: 0x61cb2cbbe998>
## .. .. .. ..$ fcall : language "f"(Intercept, model = BRU_Intercept_main_model, ngroup = 1, nrep = 1, values = BRU_Intercept_values)
## .. .. .. ..$ mapper :List of 6
## .. .. .. .. ..$ mappers :List of 2
## .. .. .. .. .. ..$ mapper:List of 9
## .. .. .. .. .. .. ..$ mappers :List of 3
## .. .. .. .. .. .. .. ..$ main : list()
## .. .. .. .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_linear" "bru_mapper" "list"
## .. .. .. .. .. .. .. ..$ group :List of 1
## .. .. .. .. .. .. .. .. ..$ n: num 1
## .. .. .. .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_index" "bru_mapper" "list"
## .. .. .. .. .. .. .. ..$ replicate:List of 1
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## .. .. .. .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_index" "bru_mapper" "list"
## .. .. .. .. .. .. ..$ n_multi :List of 3
## .. .. .. .. .. .. .. ..$ main : int 1
## .. .. .. .. .. .. .. ..$ group : num 1
## .. .. .. .. .. .. .. ..$ replicate: num 1
## .. .. .. .. .. .. ..$ n_inla_multi :List of 3
## .. .. .. .. .. .. .. ..$ main : int 1
## .. .. .. .. .. .. .. ..$ group : num 1
## .. .. .. .. .. .. .. ..$ replicate: num 1
## .. .. .. .. .. .. ..$ values_multi :List of 3
## .. .. .. .. .. .. .. ..$ main : num 1
## .. .. .. .. .. .. .. ..$ group : int 1
## .. .. .. .. .. .. .. ..$ replicate: int 1
## .. .. .. .. .. .. ..$ values_inla_multi:List of 3
## .. .. .. .. .. .. .. ..$ main : num 1
## .. .. .. .. .. .. .. ..$ group : int 1
## .. .. .. .. .. .. .. ..$ replicate: int 1
## .. .. .. .. .. .. ..$ is_linear_multi :List of 3
## .. .. .. .. .. .. .. ..$ main : logi TRUE
## .. .. .. .. .. .. .. ..$ group : logi TRUE
## .. .. .. .. .. .. .. ..$ replicate: logi TRUE
## .. .. .. .. .. .. ..$ n : num 1
## .. .. .. .. .. .. ..$ n_inla : num 1
## .. .. .. .. .. .. ..$ is_linear : logi TRUE
## .. .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_multi" "bru_mapper" "list"
## .. .. .. .. .. ..$ scale : list()
## .. .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_scale" "bru_mapper" "list"
## .. .. .. .. ..$ : Named logi [1:2] TRUE TRUE
## .. .. .. .. .. ..- attr(*, "names")= chr [1:2] "mapper" "scale"
## .. .. .. .. ..$ is_linear: logi TRUE
## .. .. .. .. ..$ n_multi : Named int [1:2] 1 NA
## .. .. .. .. .. ..- attr(*, "names")= chr [1:2] "mapper" "scale"
## .. .. .. .. ..$ n : num 1
## .. .. .. .. ..$ names : chr [1:2] "mapper" "scale"
## .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_pipe" "bru_mapper" "list"
## .. .. .. ..- attr(*, "class")= chr [1:2] "component" "list"
## .. .. ..$ SpeedLimit:List of 12
## .. .. .. ..$ label : chr "SpeedLimit"
## .. .. .. ..$ inla.formula:Class 'formula' language ~. + f(SpeedLimit, model = BRU_SpeedLimit_main_model, ngroup = 1, nrep = 1, values = BRU_SpeedLimit_values)
## .. .. .. .. .. ..- attr(*, ".Environment")=<environment: R_GlobalEnv>
## .. .. .. ..$ main :List of 8
## .. .. .. .. ..$ input :List of 4
## .. .. .. .. .. ..$ input : symbol SpeedLimit
## .. .. .. .. .. ..$ label : chr "SpeedLimit"
## .. .. .. .. .. ..$ layer : NULL
## .. .. .. .. .. ..$ selector: NULL
## .. .. .. .. .. ..- attr(*, "class")= chr [1:2] "bru_input" "list"
## .. .. .. .. ..$ mapper : list()
## .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_linear" "bru_mapper" "list"
## .. .. .. .. ..$ model : chr "linear"
## .. .. .. .. ..$ type : chr "linear"
## .. .. .. .. ..$ n : int 1
## .. .. .. .. ..$ values : num 1
## .. .. .. .. ..$ season.length : NULL
## .. .. .. .. ..$ factor_mapping: NULL
## .. .. .. .. ..- attr(*, "class")= chr [1:2] "bru_subcomponent" "list"
## .. .. .. ..$ group :List of 8
## .. .. .. .. ..$ input :List of 4
## .. .. .. .. .. ..$ input : int 1
## .. .. .. .. .. ..$ label : chr "SpeedLimit.group"
## .. .. .. .. .. ..$ layer : NULL
## .. .. .. .. .. ..$ selector: NULL
## .. .. .. .. .. ..- attr(*, "class")= chr [1:2] "bru_input" "list"
## .. .. .. .. ..$ mapper :List of 1
## .. .. .. .. .. ..$ n: num 1
## .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_index" "bru_mapper" "list"
## .. .. .. .. ..$ model : chr "exchangeable"
## .. .. .. .. ..$ type : chr "exchangeable"
## .. .. .. .. ..$ n : num 1
## .. .. .. .. ..$ values : int 1
## .. .. .. .. ..$ season.length : NULL
## .. .. .. .. ..$ factor_mapping: NULL
## .. .. .. .. ..- attr(*, "class")= chr [1:2] "bru_subcomponent" "list"
## .. .. .. ..$ replicate :List of 8
## .. .. .. .. ..$ input :List of 4
## .. .. .. .. .. ..$ input : int 1
## .. .. .. .. .. ..$ label : chr "SpeedLimit.repl"
## .. .. .. .. .. ..$ layer : NULL
## .. .. .. .. .. ..$ selector: NULL
## .. .. .. .. .. ..- attr(*, "class")= chr [1:2] "bru_input" "list"
## .. .. .. .. ..$ mapper :List of 1
## .. .. .. .. .. ..$ n: num 1
## .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_index" "bru_mapper" "list"
## .. .. .. .. ..$ model : chr "iid"
## .. .. .. .. ..$ type : chr "iid"
## .. .. .. .. ..$ n : num 1
## .. .. .. .. ..$ values : int 1
## .. .. .. .. ..$ season.length : NULL
## .. .. .. .. ..$ factor_mapping: NULL
## .. .. .. .. ..- attr(*, "class")= chr [1:2] "bru_subcomponent" "list"
## .. .. .. ..$ weights : NULL
## .. .. .. ..$ copy : NULL
## .. .. .. ..$ marginal : NULL
## .. .. .. ..$ env :<environment: R_GlobalEnv>
## .. .. .. ..$ env_extra :<environment: 0x61cb2cb75130>
## .. .. .. ..$ fcall : language "f"(SpeedLimit, model = BRU_SpeedLimit_main_model, ngroup = 1, nrep = 1, values = BRU_SpeedLimit_values)
## .. .. .. ..$ mapper :List of 6
## .. .. .. .. ..$ mappers :List of 2
## .. .. .. .. .. ..$ mapper:List of 9
## .. .. .. .. .. .. ..$ mappers :List of 3
## .. .. .. .. .. .. .. ..$ main : list()
## .. .. .. .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_linear" "bru_mapper" "list"
## .. .. .. .. .. .. .. ..$ group :List of 1
## .. .. .. .. .. .. .. .. ..$ n: num 1
## .. .. .. .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_index" "bru_mapper" "list"
## .. .. .. .. .. .. .. ..$ replicate:List of 1
## .. .. .. .. .. .. .. .. ..$ n: num 1
## .. .. .. .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_index" "bru_mapper" "list"
## .. .. .. .. .. .. ..$ n_multi :List of 3
## .. .. .. .. .. .. .. ..$ main : int 1
## .. .. .. .. .. .. .. ..$ group : num 1
## .. .. .. .. .. .. .. ..$ replicate: num 1
## .. .. .. .. .. .. ..$ n_inla_multi :List of 3
## .. .. .. .. .. .. .. ..$ main : int 1
## .. .. .. .. .. .. .. ..$ group : num 1
## .. .. .. .. .. .. .. ..$ replicate: num 1
## .. .. .. .. .. .. ..$ values_multi :List of 3
## .. .. .. .. .. .. .. ..$ main : num 1
## .. .. .. .. .. .. .. ..$ group : int 1
## .. .. .. .. .. .. .. ..$ replicate: int 1
## .. .. .. .. .. .. ..$ values_inla_multi:List of 3
## .. .. .. .. .. .. .. ..$ main : num 1
## .. .. .. .. .. .. .. ..$ group : int 1
## .. .. .. .. .. .. .. ..$ replicate: int 1
## .. .. .. .. .. .. ..$ is_linear_multi :List of 3
## .. .. .. .. .. .. .. ..$ main : logi TRUE
## .. .. .. .. .. .. .. ..$ group : logi TRUE
## .. .. .. .. .. .. .. ..$ replicate: logi TRUE
## .. .. .. .. .. .. ..$ n : num 1
## .. .. .. .. .. .. ..$ n_inla : num 1
## .. .. .. .. .. .. ..$ is_linear : logi TRUE
## .. .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_multi" "bru_mapper" "list"
## .. .. .. .. .. ..$ scale : list()
## .. .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_scale" "bru_mapper" "list"
## .. .. .. .. ..$ : Named logi [1:2] TRUE TRUE
## .. .. .. .. .. ..- attr(*, "names")= chr [1:2] "mapper" "scale"
## .. .. .. .. ..$ is_linear: logi TRUE
## .. .. .. .. ..$ n_multi : Named int [1:2] 1 NA
## .. .. .. .. .. ..- attr(*, "names")= chr [1:2] "mapper" "scale"
## .. .. .. .. ..$ n : num 1
## .. .. .. .. ..$ names : chr [1:2] "mapper" "scale"
## .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_pipe" "bru_mapper" "list"
## .. .. .. ..- attr(*, "class")= chr [1:2] "component" "list"
## .. .. ..$ field :List of 12
## .. .. .. ..$ label : chr "field"
## .. .. .. ..$ inla.formula:Class 'formula' language ~. + f(field, model = BRU_field_main_model, replicate = field.repl, ngroup = 1, nrep = 4L, values = BRU_field_values)
## .. .. .. .. .. ..- attr(*, ".Environment")=<environment: R_GlobalEnv>
## .. .. .. ..$ main :List of 8
## .. .. .. .. ..$ input :List of 4
## .. .. .. .. .. ..$ input : symbol loc
## .. .. .. .. .. ..$ label : chr "field"
## .. .. .. .. .. ..$ layer : NULL
## .. .. .. .. .. ..$ selector: NULL
## .. .. .. .. .. ..- attr(*, "class")= chr [1:2] "bru_input" "list"
## .. .. .. .. ..$ mapper :List of 1
## .. .. .. .. .. ..$ model:List of 20
## .. .. .. .. .. .. ..$ f :List of 3
## .. .. .. .. .. .. .. ..$ model : chr "cgeneric"
## .. .. .. .. .. .. .. ..$ n : int 41796
## .. .. .. .. .. .. .. ..$ cgeneric:List of 5
## .. .. .. .. .. .. .. .. ..$ model: chr "inla_cgeneric_rspde_stat_general_model"
## .. .. .. .. .. .. .. .. ..$ shlib: chr "/home/rierasl/R/x86_64-pc-linux-gnu-library/4.4/INLA/bin/linux/64bit/external/rSPDE/librSPDE.so"
## .. .. .. .. .. .. .. .. ..$ n : int 41796
## .. .. .. .. .. .. .. .. ..$ debug: logi FALSE
## .. .. .. .. .. .. .. .. ..$ data :List of 5
## .. .. .. .. .. .. .. .. .. ..$ ints :List of 5
## .. .. .. .. .. .. .. .. .. .. ..$ n : int 41796
## .. .. .. .. .. .. .. .. .. .. ..$ debug : int 0
## .. .. .. .. .. .. .. .. .. .. ..$ graph_opt_i: int [1:186659] 0 0 0 0 0 0 0 0 0 1 ...
## .. .. .. .. .. .. .. .. .. .. ..$ graph_opt_j: int [1:186659] 0 1 805 5399 5681 8781 11429 11463 13882 1 ...
## .. .. .. .. .. .. .. .. .. .. ..$ rspde.order: int 2
## .. .. .. .. .. .. .. .. .. ..$ doubles :List of 11
## .. .. .. .. .. .. .. .. .. .. ..$ d : num 1
## .. .. .. .. .. .. .. .. .. .. ..$ nu.upper.bound : num 1.5
## .. .. .. .. .. .. .. .. .. .. ..$ matrices_less : num [1:143229] 0.0534 0 0 0 0 ...
## .. .. .. .. .. .. .. .. .. .. ..$ matrices_full : num [1:277832] 0.0534 0 0 0 0 ...
## .. .. .. .. .. .. .. .. .. .. ..$ start.theta : num [1:2] 0 1.35
## .. .. .. .. .. .. .. .. .. .. ..$ theta.prior.mean : num [1:2] 0 1.35
## .. .. .. .. .. .. .. .. .. .. ..$ prior.nu.loglocation: num -0.288
## .. .. .. .. .. .. .. .. .. .. ..$ prior.nu.mean : num 0.75
## .. .. .. .. .. .. .. .. .. .. ..$ prior.nu.prec : num 3
## .. .. .. .. .. .. .. .. .. .. ..$ prior.nu.logscale : num 1
## .. .. .. .. .. .. .. .. .. .. ..$ start.nu : num 0.75
## .. .. .. .. .. .. .. .. .. ..$ characters:List of 5
## .. .. .. .. .. .. .. .. .. .. ..$ model : chr "inla_cgeneric_rspde_stat_general_model"
## .. .. .. .. .. .. .. .. .. .. ..$ shlib : chr "/home/rierasl/R/x86_64-pc-linux-gnu-library/4.4/INLA/bin/linux/64bit/external/rSPDE/librSPDE.so"
## .. .. .. .. .. .. .. .. .. .. ..$ prior.nu.dist : chr "lognormal"
## .. .. .. .. .. .. .. .. .. .. ..$ parameterization : chr "matern"
## .. .. .. .. .. .. .. .. .. .. ..$ prior.theta.param: chr "theta"
## .. .. .. .. .. .. .. .. .. ..$ matrices :List of 2
## .. .. .. .. .. .. .. .. .. .. ..$ rational_table : num [1:5996] 999 6 0.001 0.412 0.005 ...
## .. .. .. .. .. .. .. .. .. .. ..$ theta.prior.prec: num [1:6] 2 2 0.1 0 0 0.1
## .. .. .. .. .. .. .. .. .. ..$ smatrices : list()
## .. .. .. .. .. .. .. .. ..- attr(*, "class")= chr "inla.cgeneric"
## .. .. .. .. .. .. ..$ cgeneric_type : chr "general"
## .. .. .. .. .. .. ..$ theta.prior.mean : num [1:2] 0 1.35
## .. .. .. .. .. .. ..$ prior.nu :List of 4
## .. .. .. .. .. .. .. ..$ loglocation: num -0.288
## .. .. .. .. .. .. .. ..$ mean : num 0.75
## .. .. .. .. .. .. .. ..$ prec : num 3
## .. .. .. .. .. .. .. ..$ logscale : num 1
## .. .. .. .. .. .. ..$ theta.prior.prec : num [1:2, 1:2] 0.1 0 0 0.1
## .. .. .. .. .. .. ..$ start.nu : num 0.75
## .. .. .. .. .. .. ..$ integer.nu : logi FALSE
## .. .. .. .. .. .. ..$ start.theta : num [1:2] 0 1.35
## .. .. .. .. .. .. ..$ stationary : logi TRUE
## .. .. .. .. .. .. ..$ rspde.order : num 2
## .. .. .. .. .. .. ..$ dim : num 1
## .. .. .. .. .. .. ..$ est_nu : logi TRUE
## .. .. .. .. .. .. ..$ nu.upper.bound : num 1.5
## .. .. .. .. .. .. ..$ prior.nu.dist : chr "lognormal"
## .. .. .. .. .. .. ..$ debug : logi FALSE
## .. .. .. .. .. .. ..$ type.rational.approx: chr "chebfun"
## .. .. .. .. .. .. ..$ mesh :Classes 'metric_graph', 'R6' <metric_graph>
## Public:
## add_mesh_observations: function (data = NULL, group = NULL)
## add_observations: function (data = NULL, edge_number = "edge_number", distance_on_edge = "distance_on_edge",
## build_mesh: function (h = NULL, n = NULL, continuous = TRUE, continuous.outs = FALSE,
## buildC: function (alpha = 2, edge_constraint = FALSE)
## buildDirectionalConstraints: function (alpha = 1)
## C: NULL
## characteristics: list
## check_distance_consistency: function ()
## check_euclidean: function ()
## clear_observations: function ()
## clone: function (deep = FALSE)
## CoB: NULL
## compute_characteristics: function (check_euclidean = FALSE)
## compute_fem: function (petrov = FALSE)
## compute_geodist: function (full = FALSE, obs = TRUE, group = NULL, verbose = 0)
## compute_geodist_mesh: function ()
## compute_geodist_PtE: function (PtE, normalized = TRUE, include_vertices = TRUE, verbose = 0)
## compute_laplacian: function (full = FALSE, obs = TRUE, group = NULL, verbose = 0)
## compute_PtE_edges: function ()
## compute_resdist: function (full = FALSE, obs = TRUE, group = NULL, check_euclidean = FALSE,
## compute_resdist_mesh: function ()
## compute_resdist_PtE: function (PtE, normalized = TRUE, include_vertices = FALSE, check_euclidean = FALSE,
## coordinates: function (PtE = NULL, XY = NULL, normalized = TRUE)
## drop_na: function (...)
## E: 1 3 5 7 9 9 10 12 13 14 15 12 18 19 21 20 22 24 26 28 30 ...
## edge_lengths: 0.0820202978316493 0.13610246403764 0.07378151878521 0.0 ...
## edges: metric_graph_edges
## edgeweight_to_data: function (loc = NULL, mesh = FALSE, data_loc = FALSE, weight_col = NULL,
## fem_basis: function (PtE)
## filter: function (..., .drop_na = FALSE, .drop_all_na = TRUE)
## geo_dist: list
## get_data: function (group = NULL, tibble = TRUE, drop_na = FALSE, drop_all_na = TRUE)
## get_degrees: function (which = "degree")
## get_edge_lengths: function (unit = NULL)
## get_edge_weights: function (data.frame = FALSE, tibble = TRUE)
## get_groups: function (get_cols = FALSE)
## get_initial_graph: function ()
## get_locations: function ()
## get_mesh_locations: function (bru = FALSE, loc = NULL, normalized = TRUE)
## get_PtE: function ()
## get_vertices_incomp_dir: function ()
## initialize: function (edges = NULL, V = NULL, E = NULL, vertex_unit = NULL,
## is_tree: function ()
## Laplacian: NULL
## mesh: list
## mesh_A: function (PtE)
## mutate: function (..., .drop_na = FALSE, .drop_all_na = TRUE)
## nE: 11104
## nV: 8781
## observation_to_vertex: function (tolerance = 1e-15, mesh_warning = TRUE)
## plot: function (data = NULL, newdata = NULL, group = 1, plotly = FALSE,
## plot_connections: function ()
## plot_function: function (data = NULL, newdata = NULL, group = 1, X = NULL, plotly = FALSE,
## plot_movie: function (X, plotly = TRUE, vertex_size = 5, vertex_color = "black",
## print: function ()
## process_data: function (data = NULL, edge_number = "edge_number", distance_on_edge = "distance_on_edge",
## prune_vertices: function (check_weights = TRUE, verbose = FALSE)
## PtV: NULL
## res_dist: NULL
## select: function (..., .drop_na = FALSE, .drop_all_na = TRUE)
## set_edge_weights: function (weights = rep(1, self$nE), kirchhoff_weights = NULL)
## summarise: function (..., .include_graph_groups = FALSE, .groups = NULL,
## summary: function (messages = FALSE, compute_characteristics = TRUE, check_euclidean = TRUE,
## V: -122.40171 -122.40078 -122.44449 -122.44331 -122.41216 - ...
## vertices: metric_graph_vertices
## VtEfirst: function ()
## Private:
## A: function (group = NULL, obs_to_vert = FALSE, drop_na = FALSE,
## add_vertices: function (PtE, tolerance = 1e-10, verbose)
## addinfo: FALSE
## clear_initial_info: function ()
## compute_degrees: function ()
## compute_laplacian_PtE: function (PtE, normalized = TRUE, verbose = verbose)
## compute_lengths: function (longlat, unit, crs, proj4string, which_longlat, vertex_unit,
## connected: TRUE
## coordinates_multiple_snaps: function (XY, tolerance, verbose = verbose, crs, proj4string,
## create_update_vertices: function ()
## crs: crs
## data: metric_graph_data, list
## edge_weights: tbl_df, tbl, data.frame
## find_edge_edge_points: function (tol, verbose, crs, proj4string, longlat, fact, which_longlat)
## find_mesh_bc: function ()
## get_edge_weights_internal: function (data.frame = FALSE)
## group_col: .group
## initial_edges_added: NULL
## initial_graph: metric_graph, R6
## kirchhoff_weights: NULL
## length_unit: km
## line_to_vertex: function (tolerance = 0, longlat = FALSE, fact, verbose, crs,
## longlat: TRUE
## merge_close_vertices: function (tolerance, fact)
## merge.all.deg2: function ()
## mesh_merge_deg2: function ()
## mesh_merge_outs: function ()
## move_V_first: function ()
## plot_2d: function (line_width = 0.1, marker_size = 1, vertex_color = "black",
## plot_3d: function (line_width = 1, marker_size = 1, vertex_color = "rgb(0,0,0)",
## proj4string: NULL
## prune_warning: FALSE
## pruned: FALSE
## PtE_to_mesh: function (PtE)
## ref_edges: 1 5502 2 359 3 4077 4 5117 5 7 5419 8 9 10 11 4817 4613 ...
## remove_circles: function (threshold, verbose, longlat, unit, crs, proj4string,
## remove.first.deg2: function (res)
## set_first_weights: function (weights = rep(1, self$nE))
## set_petrov_matrices: function ()
## split_edge: function (Ei, t, tolerance = 0)
## temp_PtE: NULL
## tolerance: list
## transform: FALSE
## vertex_unit: degrees
## which_longlat: sf
## .. .. .. .. .. .. ..$ fem_mesh :List of 5
## .. .. .. .. .. .. .. ..$ c0:Formal class 'dgTMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. .. .. .. .. ..@ i : int [1:13932] 0 1 2 3 4 5 6 7 8 9 ...
## .. .. .. .. .. .. .. .. .. ..@ j : int [1:13932] 0 1 2 3 4 5 6 7 8 9 ...
## .. .. .. .. .. .. .. .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. .. .. .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. ..@ x : num [1:13932] 0.0534 0.0776 0.0408 0.0457 0.0367 ...
## .. .. .. .. .. .. .. .. .. ..@ factors : list()
## .. .. .. .. .. .. .. ..$ g1:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. .. .. .. .. ..@ i : int [1:44204] 0 5681 8781 11463 1 8781 11429 11463 13882 2 ...
## .. .. .. .. .. .. .. .. .. ..@ p : int [1:13933] 0 4 9 12 15 18 23 26 29 34 ...
## .. .. .. .. .. .. .. .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. .. .. .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. ..@ x : num [1:44204] 210.6 -161.9 -24.4 -24.4 103.4 ...
## .. .. .. .. .. .. .. .. .. ..@ factors : list()
## .. .. .. .. .. .. .. ..$ g2:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. .. .. .. .. ..@ i : int [1:81554] 0 1 5399 5681 8781 11463 0 1 4450 8781 ...
## .. .. .. .. .. .. .. .. .. ..@ p : int [1:13933] 0 6 13 18 23 28 37 42 47 56 ...
## .. .. .. .. .. .. .. .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. .. .. .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. ..@ x : num [1:81554] 1731368 28997 607384 -2117274 -125237 ...
## .. .. .. .. .. .. .. .. .. ..@ factors : list()
## .. .. .. .. .. .. .. ..$ g3:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. .. .. .. .. ..@ i : int [1:124984] 0 1 805 5399 5681 8781 11429 11463 13882 0 ...
## .. .. .. .. .. .. .. .. .. ..@ p : int [1:13933] 0 9 18 25 32 43 56 65 72 85 ...
## .. .. .. .. .. .. .. .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. .. .. .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. ..@ x : num [1:124984] 1.84e+10 1.88e+08 -4.79e+08 9.57e+09 -2.57e+10 ...
## .. .. .. .. .. .. .. .. .. ..@ factors : list()
## .. .. .. .. .. .. .. ..$ g4:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. .. .. .. .. ..@ i : int [1:175232] 0 1 804 805 4450 5399 5681 8781 11429 11463 ...
## .. .. .. .. .. .. .. .. .. ..@ p : int [1:13933] 0 11 23 32 41 58 76 89 98 116 ...
## .. .. .. .. .. .. .. .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. .. .. .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. ..@ x : num [1:175232] 2.12e+14 1.39e+12 8.54e+11 -8.78e+12 1.53e+10 ...
## .. .. .. .. .. .. .. .. .. ..@ factors : list()
## .. .. .. .. .. .. ..$ parameterization : chr "matern"
## .. .. .. .. .. .. ..$ n.spde : int 13932
## .. .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "rspde_metric_graph" "inla_rspde" "inla.cgeneric"
## .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_inla_rspde" "bru_mapper" "list"
## .. .. .. .. ..$ model :List of 20
## .. .. .. .. .. ..$ f :List of 3
## .. .. .. .. .. .. ..$ model : chr "cgeneric"
## .. .. .. .. .. .. ..$ n : int 41796
## .. .. .. .. .. .. ..$ cgeneric:List of 5
## .. .. .. .. .. .. .. ..$ model: chr "inla_cgeneric_rspde_stat_general_model"
## .. .. .. .. .. .. .. ..$ shlib: chr "/home/rierasl/R/x86_64-pc-linux-gnu-library/4.4/INLA/bin/linux/64bit/external/rSPDE/librSPDE.so"
## .. .. .. .. .. .. .. ..$ n : int 41796
## .. .. .. .. .. .. .. ..$ debug: logi FALSE
## .. .. .. .. .. .. .. ..$ data :List of 5
## .. .. .. .. .. .. .. .. ..$ ints :List of 5
## .. .. .. .. .. .. .. .. .. ..$ n : int 41796
## .. .. .. .. .. .. .. .. .. ..$ debug : int 0
## .. .. .. .. .. .. .. .. .. ..$ graph_opt_i: int [1:186659] 0 0 0 0 0 0 0 0 0 1 ...
## .. .. .. .. .. .. .. .. .. ..$ graph_opt_j: int [1:186659] 0 1 805 5399 5681 8781 11429 11463 13882 1 ...
## .. .. .. .. .. .. .. .. .. ..$ rspde.order: int 2
## .. .. .. .. .. .. .. .. ..$ doubles :List of 11
## .. .. .. .. .. .. .. .. .. ..$ d : num 1
## .. .. .. .. .. .. .. .. .. ..$ nu.upper.bound : num 1.5
## .. .. .. .. .. .. .. .. .. ..$ matrices_less : num [1:143229] 0.0534 0 0 0 0 ...
## .. .. .. .. .. .. .. .. .. ..$ matrices_full : num [1:277832] 0.0534 0 0 0 0 ...
## .. .. .. .. .. .. .. .. .. ..$ start.theta : num [1:2] 0 1.35
## .. .. .. .. .. .. .. .. .. ..$ theta.prior.mean : num [1:2] 0 1.35
## .. .. .. .. .. .. .. .. .. ..$ prior.nu.loglocation: num -0.288
## .. .. .. .. .. .. .. .. .. ..$ prior.nu.mean : num 0.75
## .. .. .. .. .. .. .. .. .. ..$ prior.nu.prec : num 3
## .. .. .. .. .. .. .. .. .. ..$ prior.nu.logscale : num 1
## .. .. .. .. .. .. .. .. .. ..$ start.nu : num 0.75
## .. .. .. .. .. .. .. .. ..$ characters:List of 5
## .. .. .. .. .. .. .. .. .. ..$ model : chr "inla_cgeneric_rspde_stat_general_model"
## .. .. .. .. .. .. .. .. .. ..$ shlib : chr "/home/rierasl/R/x86_64-pc-linux-gnu-library/4.4/INLA/bin/linux/64bit/external/rSPDE/librSPDE.so"
## .. .. .. .. .. .. .. .. .. ..$ prior.nu.dist : chr "lognormal"
## .. .. .. .. .. .. .. .. .. ..$ parameterization : chr "matern"
## .. .. .. .. .. .. .. .. .. ..$ prior.theta.param: chr "theta"
## .. .. .. .. .. .. .. .. ..$ matrices :List of 2
## .. .. .. .. .. .. .. .. .. ..$ rational_table : num [1:5996] 999 6 0.001 0.412 0.005 ...
## .. .. .. .. .. .. .. .. .. ..$ theta.prior.prec: num [1:6] 2 2 0.1 0 0 0.1
## .. .. .. .. .. .. .. .. ..$ smatrices : list()
## .. .. .. .. .. .. .. ..- attr(*, "class")= chr "inla.cgeneric"
## .. .. .. .. .. ..$ cgeneric_type : chr "general"
## .. .. .. .. .. ..$ theta.prior.mean : num [1:2] 0 1.35
## .. .. .. .. .. ..$ prior.nu :List of 4
## .. .. .. .. .. .. ..$ loglocation: num -0.288
## .. .. .. .. .. .. ..$ mean : num 0.75
## .. .. .. .. .. .. ..$ prec : num 3
## .. .. .. .. .. .. ..$ logscale : num 1
## .. .. .. .. .. ..$ theta.prior.prec : num [1:2, 1:2] 0.1 0 0 0.1
## .. .. .. .. .. ..$ start.nu : num 0.75
## .. .. .. .. .. ..$ integer.nu : logi FALSE
## .. .. .. .. .. ..$ start.theta : num [1:2] 0 1.35
## .. .. .. .. .. ..$ stationary : logi TRUE
## .. .. .. .. .. ..$ rspde.order : num 2
## .. .. .. .. .. ..$ dim : num 1
## .. .. .. .. .. ..$ est_nu : logi TRUE
## .. .. .. .. .. ..$ nu.upper.bound : num 1.5
## .. .. .. .. .. ..$ prior.nu.dist : chr "lognormal"
## .. .. .. .. .. ..$ debug : logi FALSE
## .. .. .. .. .. ..$ type.rational.approx: chr "chebfun"
## .. .. .. .. .. ..$ mesh :Classes 'metric_graph', 'R6' <metric_graph>
## Public:
## add_mesh_observations: function (data = NULL, group = NULL)
## add_observations: function (data = NULL, edge_number = "edge_number", distance_on_edge = "distance_on_edge",
## build_mesh: function (h = NULL, n = NULL, continuous = TRUE, continuous.outs = FALSE,
## buildC: function (alpha = 2, edge_constraint = FALSE)
## buildDirectionalConstraints: function (alpha = 1)
## C: NULL
## characteristics: list
## check_distance_consistency: function ()
## check_euclidean: function ()
## clear_observations: function ()
## clone: function (deep = FALSE)
## CoB: NULL
## compute_characteristics: function (check_euclidean = FALSE)
## compute_fem: function (petrov = FALSE)
## compute_geodist: function (full = FALSE, obs = TRUE, group = NULL, verbose = 0)
## compute_geodist_mesh: function ()
## compute_geodist_PtE: function (PtE, normalized = TRUE, include_vertices = TRUE, verbose = 0)
## compute_laplacian: function (full = FALSE, obs = TRUE, group = NULL, verbose = 0)
## compute_PtE_edges: function ()
## compute_resdist: function (full = FALSE, obs = TRUE, group = NULL, check_euclidean = FALSE,
## compute_resdist_mesh: function ()
## compute_resdist_PtE: function (PtE, normalized = TRUE, include_vertices = FALSE, check_euclidean = FALSE,
## coordinates: function (PtE = NULL, XY = NULL, normalized = TRUE)
## drop_na: function (...)
## E: 1 3 5 7 9 9 10 12 13 14 15 12 18 19 21 20 22 24 26 28 30 ...
## edge_lengths: 0.0820202978316493 0.13610246403764 0.07378151878521 0.0 ...
## edges: metric_graph_edges
## edgeweight_to_data: function (loc = NULL, mesh = FALSE, data_loc = FALSE, weight_col = NULL,
## fem_basis: function (PtE)
## filter: function (..., .drop_na = FALSE, .drop_all_na = TRUE)
## geo_dist: list
## get_data: function (group = NULL, tibble = TRUE, drop_na = FALSE, drop_all_na = TRUE)
## get_degrees: function (which = "degree")
## get_edge_lengths: function (unit = NULL)
## get_edge_weights: function (data.frame = FALSE, tibble = TRUE)
## get_groups: function (get_cols = FALSE)
## get_initial_graph: function ()
## get_locations: function ()
## get_mesh_locations: function (bru = FALSE, loc = NULL, normalized = TRUE)
## get_PtE: function ()
## get_vertices_incomp_dir: function ()
## initialize: function (edges = NULL, V = NULL, E = NULL, vertex_unit = NULL,
## is_tree: function ()
## Laplacian: NULL
## mesh: list
## mesh_A: function (PtE)
## mutate: function (..., .drop_na = FALSE, .drop_all_na = TRUE)
## nE: 11104
## nV: 8781
## observation_to_vertex: function (tolerance = 1e-15, mesh_warning = TRUE)
## plot: function (data = NULL, newdata = NULL, group = 1, plotly = FALSE,
## plot_connections: function ()
## plot_function: function (data = NULL, newdata = NULL, group = 1, X = NULL, plotly = FALSE,
## plot_movie: function (X, plotly = TRUE, vertex_size = 5, vertex_color = "black",
## print: function ()
## process_data: function (data = NULL, edge_number = "edge_number", distance_on_edge = "distance_on_edge",
## prune_vertices: function (check_weights = TRUE, verbose = FALSE)
## PtV: NULL
## res_dist: NULL
## select: function (..., .drop_na = FALSE, .drop_all_na = TRUE)
## set_edge_weights: function (weights = rep(1, self$nE), kirchhoff_weights = NULL)
## summarise: function (..., .include_graph_groups = FALSE, .groups = NULL,
## summary: function (messages = FALSE, compute_characteristics = TRUE, check_euclidean = TRUE,
## V: -122.40171 -122.40078 -122.44449 -122.44331 -122.41216 - ...
## vertices: metric_graph_vertices
## VtEfirst: function ()
## Private:
## A: function (group = NULL, obs_to_vert = FALSE, drop_na = FALSE,
## add_vertices: function (PtE, tolerance = 1e-10, verbose)
## addinfo: FALSE
## clear_initial_info: function ()
## compute_degrees: function ()
## compute_laplacian_PtE: function (PtE, normalized = TRUE, verbose = verbose)
## compute_lengths: function (longlat, unit, crs, proj4string, which_longlat, vertex_unit,
## connected: TRUE
## coordinates_multiple_snaps: function (XY, tolerance, verbose = verbose, crs, proj4string,
## create_update_vertices: function ()
## crs: crs
## data: metric_graph_data, list
## edge_weights: tbl_df, tbl, data.frame
## find_edge_edge_points: function (tol, verbose, crs, proj4string, longlat, fact, which_longlat)
## find_mesh_bc: function ()
## get_edge_weights_internal: function (data.frame = FALSE)
## group_col: .group
## initial_edges_added: NULL
## initial_graph: metric_graph, R6
## kirchhoff_weights: NULL
## length_unit: km
## line_to_vertex: function (tolerance = 0, longlat = FALSE, fact, verbose, crs,
## longlat: TRUE
## merge_close_vertices: function (tolerance, fact)
## merge.all.deg2: function ()
## mesh_merge_deg2: function ()
## mesh_merge_outs: function ()
## move_V_first: function ()
## plot_2d: function (line_width = 0.1, marker_size = 1, vertex_color = "black",
## plot_3d: function (line_width = 1, marker_size = 1, vertex_color = "rgb(0,0,0)",
## proj4string: NULL
## prune_warning: FALSE
## pruned: FALSE
## PtE_to_mesh: function (PtE)
## ref_edges: 1 5502 2 359 3 4077 4 5117 5 7 5419 8 9 10 11 4817 4613 ...
## remove_circles: function (threshold, verbose, longlat, unit, crs, proj4string,
## remove.first.deg2: function (res)
## set_first_weights: function (weights = rep(1, self$nE))
## set_petrov_matrices: function ()
## split_edge: function (Ei, t, tolerance = 0)
## temp_PtE: NULL
## tolerance: list
## transform: FALSE
## vertex_unit: degrees
## which_longlat: sf
## .. .. .. .. .. ..$ fem_mesh :List of 5
## .. .. .. .. .. .. ..$ c0:Formal class 'dgTMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. .. .. .. ..@ i : int [1:13932] 0 1 2 3 4 5 6 7 8 9 ...
## .. .. .. .. .. .. .. .. ..@ j : int [1:13932] 0 1 2 3 4 5 6 7 8 9 ...
## .. .. .. .. .. .. .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. .. .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. ..@ x : num [1:13932] 0.0534 0.0776 0.0408 0.0457 0.0367 ...
## .. .. .. .. .. .. .. .. ..@ factors : list()
## .. .. .. .. .. .. ..$ g1:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. .. .. .. ..@ i : int [1:44204] 0 5681 8781 11463 1 8781 11429 11463 13882 2 ...
## .. .. .. .. .. .. .. .. ..@ p : int [1:13933] 0 4 9 12 15 18 23 26 29 34 ...
## .. .. .. .. .. .. .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. .. .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. ..@ x : num [1:44204] 210.6 -161.9 -24.4 -24.4 103.4 ...
## .. .. .. .. .. .. .. .. ..@ factors : list()
## .. .. .. .. .. .. ..$ g2:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. .. .. .. ..@ i : int [1:81554] 0 1 5399 5681 8781 11463 0 1 4450 8781 ...
## .. .. .. .. .. .. .. .. ..@ p : int [1:13933] 0 6 13 18 23 28 37 42 47 56 ...
## .. .. .. .. .. .. .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. .. .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. ..@ x : num [1:81554] 1731368 28997 607384 -2117274 -125237 ...
## .. .. .. .. .. .. .. .. ..@ factors : list()
## .. .. .. .. .. .. ..$ g3:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. .. .. .. ..@ i : int [1:124984] 0 1 805 5399 5681 8781 11429 11463 13882 0 ...
## .. .. .. .. .. .. .. .. ..@ p : int [1:13933] 0 9 18 25 32 43 56 65 72 85 ...
## .. .. .. .. .. .. .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. .. .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. ..@ x : num [1:124984] 1.84e+10 1.88e+08 -4.79e+08 9.57e+09 -2.57e+10 ...
## .. .. .. .. .. .. .. .. ..@ factors : list()
## .. .. .. .. .. .. ..$ g4:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. .. .. .. ..@ i : int [1:175232] 0 1 804 805 4450 5399 5681 8781 11429 11463 ...
## .. .. .. .. .. .. .. .. ..@ p : int [1:13933] 0 11 23 32 41 58 76 89 98 116 ...
## .. .. .. .. .. .. .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. .. .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. ..@ x : num [1:175232] 2.12e+14 1.39e+12 8.54e+11 -8.78e+12 1.53e+10 ...
## .. .. .. .. .. .. .. .. ..@ factors : list()
## .. .. .. .. .. ..$ parameterization : chr "matern"
## .. .. .. .. .. ..$ n.spde : int 13932
## .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "rspde_metric_graph" "inla_rspde" "inla.cgeneric"
## .. .. .. .. ..$ type : chr "cgeneric"
## .. .. .. .. ..$ n : num 41796
## .. .. .. .. ..$ values : int [1:41796] 1 2 3 4 5 6 7 8 9 10 ...
## .. .. .. .. ..$ season.length : NULL
## .. .. .. .. ..$ factor_mapping: NULL
## .. .. .. .. ..- attr(*, "class")= chr [1:2] "bru_subcomponent" "list"
## .. .. .. ..$ group :List of 8
## .. .. .. .. ..$ input :List of 4
## .. .. .. .. .. ..$ input : int 1
## .. .. .. .. .. ..$ label : chr "field.group"
## .. .. .. .. .. ..$ layer : NULL
## .. .. .. .. .. ..$ selector: NULL
## .. .. .. .. .. ..- attr(*, "class")= chr [1:2] "bru_input" "list"
## .. .. .. .. ..$ mapper :List of 1
## .. .. .. .. .. ..$ n: num 1
## .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_index" "bru_mapper" "list"
## .. .. .. .. ..$ model : chr "exchangeable"
## .. .. .. .. ..$ type : chr "exchangeable"
## .. .. .. .. ..$ n : num 1
## .. .. .. .. ..$ values : int 1
## .. .. .. .. ..$ season.length : NULL
## .. .. .. .. ..$ factor_mapping: NULL
## .. .. .. .. ..- attr(*, "class")= chr [1:2] "bru_subcomponent" "list"
## .. .. .. ..$ replicate :List of 8
## .. .. .. .. ..$ input :List of 4
## .. .. .. .. .. ..$ input : language data_rspde_bru_stat[["repl"]]
## .. .. .. .. .. ..$ label : chr "field.repl"
## .. .. .. .. .. ..$ layer : NULL
## .. .. .. .. .. ..$ selector: NULL
## .. .. .. .. .. ..- attr(*, "class")= chr [1:2] "bru_input" "list"
## .. .. .. .. ..$ mapper :List of 4
## .. .. .. .. .. ..$ levels : chr [1:4] "1" "2" "3" "4"
## .. .. .. .. .. ..$ factor_mapping: chr "full"
## .. .. .. .. .. ..$ indexed : logi TRUE
## .. .. .. .. .. ..$ n : int 4
## .. .. .. .. .. ..- attr(*, "class")= chr [1:4] "bru_mapper_factor_index" "bru_mapper_factor" "bru_mapper" "list"
## .. .. .. .. ..$ model : chr "iid"
## .. .. .. .. ..$ type : chr "iid"
## .. .. .. .. ..$ n : int 4
## .. .. .. .. ..$ values : int [1:4] 1 2 3 4
## .. .. .. .. ..$ season.length : NULL
## .. .. .. .. ..$ factor_mapping: NULL
## .. .. .. .. ..- attr(*, "class")= chr [1:2] "bru_subcomponent" "list"
## .. .. .. ..$ weights : NULL
## .. .. .. ..$ copy : NULL
## .. .. .. ..$ marginal : NULL
## .. .. .. ..$ env :<environment: R_GlobalEnv>
## .. .. .. ..$ env_extra :<environment: 0x61cb2cb35b78>
## .. .. .. ..$ fcall : language "f"(field, model = BRU_field_main_model, replicate = field.repl, ngroup = 1, nrep = 4L, values = BRU_field_values)
## .. .. .. ..$ mapper :List of 6
## .. .. .. .. ..$ mappers :List of 2
## .. .. .. .. .. ..$ mapper:List of 9
## .. .. .. .. .. .. ..$ mappers :List of 3
## .. .. .. .. .. .. .. ..$ main :List of 1
## .. .. .. .. .. .. .. .. ..$ model:List of 20
## .. .. .. .. .. .. .. .. .. ..$ f :List of 3
## .. .. .. .. .. .. .. .. .. .. ..$ model : chr "cgeneric"
## .. .. .. .. .. .. .. .. .. .. ..$ n : int 41796
## .. .. .. .. .. .. .. .. .. .. ..$ cgeneric:List of 5
## .. .. .. .. .. .. .. .. .. .. .. ..$ model: chr "inla_cgeneric_rspde_stat_general_model"
## .. .. .. .. .. .. .. .. .. .. .. ..$ shlib: chr "/home/rierasl/R/x86_64-pc-linux-gnu-library/4.4/INLA/bin/linux/64bit/external/rSPDE/librSPDE.so"
## .. .. .. .. .. .. .. .. .. .. .. ..$ n : int 41796
## .. .. .. .. .. .. .. .. .. .. .. ..$ debug: logi FALSE
## .. .. .. .. .. .. .. .. .. .. .. ..$ data :List of 5
## .. .. .. .. .. .. .. .. .. .. .. .. ..$ ints :List of 5
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ n : int 41796
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ debug : int 0
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ graph_opt_i: int [1:186659] 0 0 0 0 0 0 0 0 0 1 ...
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ graph_opt_j: int [1:186659] 0 1 805 5399 5681 8781 11429 11463 13882 1 ...
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ rspde.order: int 2
## .. .. .. .. .. .. .. .. .. .. .. .. ..$ doubles :List of 11
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ d : num 1
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ nu.upper.bound : num 1.5
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ matrices_less : num [1:143229] 0.0534 0 0 0 0 ...
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ matrices_full : num [1:277832] 0.0534 0 0 0 0 ...
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ start.theta : num [1:2] 0 1.35
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ theta.prior.mean : num [1:2] 0 1.35
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ prior.nu.loglocation: num -0.288
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ prior.nu.mean : num 0.75
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ prior.nu.prec : num 3
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ prior.nu.logscale : num 1
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ start.nu : num 0.75
## .. .. .. .. .. .. .. .. .. .. .. .. ..$ characters:List of 5
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ model : chr "inla_cgeneric_rspde_stat_general_model"
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ shlib : chr "/home/rierasl/R/x86_64-pc-linux-gnu-library/4.4/INLA/bin/linux/64bit/external/rSPDE/librSPDE.so"
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ prior.nu.dist : chr "lognormal"
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ parameterization : chr "matern"
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ prior.theta.param: chr "theta"
## .. .. .. .. .. .. .. .. .. .. .. .. ..$ matrices :List of 2
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ rational_table : num [1:5996] 999 6 0.001 0.412 0.005 ...
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ theta.prior.prec: num [1:6] 2 2 0.1 0 0 0.1
## .. .. .. .. .. .. .. .. .. .. .. .. ..$ smatrices : list()
## .. .. .. .. .. .. .. .. .. .. .. ..- attr(*, "class")= chr "inla.cgeneric"
## .. .. .. .. .. .. .. .. .. ..$ cgeneric_type : chr "general"
## .. .. .. .. .. .. .. .. .. ..$ theta.prior.mean : num [1:2] 0 1.35
## .. .. .. .. .. .. .. .. .. ..$ prior.nu :List of 4
## .. .. .. .. .. .. .. .. .. .. ..$ loglocation: num -0.288
## .. .. .. .. .. .. .. .. .. .. ..$ mean : num 0.75
## .. .. .. .. .. .. .. .. .. .. ..$ prec : num 3
## .. .. .. .. .. .. .. .. .. .. ..$ logscale : num 1
## .. .. .. .. .. .. .. .. .. ..$ theta.prior.prec : num [1:2, 1:2] 0.1 0 0 0.1
## .. .. .. .. .. .. .. .. .. ..$ start.nu : num 0.75
## .. .. .. .. .. .. .. .. .. ..$ integer.nu : logi FALSE
## .. .. .. .. .. .. .. .. .. ..$ start.theta : num [1:2] 0 1.35
## .. .. .. .. .. .. .. .. .. ..$ stationary : logi TRUE
## .. .. .. .. .. .. .. .. .. ..$ rspde.order : num 2
## .. .. .. .. .. .. .. .. .. ..$ dim : num 1
## .. .. .. .. .. .. .. .. .. ..$ est_nu : logi TRUE
## .. .. .. .. .. .. .. .. .. ..$ nu.upper.bound : num 1.5
## .. .. .. .. .. .. .. .. .. ..$ prior.nu.dist : chr "lognormal"
## .. .. .. .. .. .. .. .. .. ..$ debug : logi FALSE
## .. .. .. .. .. .. .. .. .. ..$ type.rational.approx: chr "chebfun"
## .. .. .. .. .. .. .. .. .. ..$ mesh :Classes 'metric_graph', 'R6' <metric_graph>
## Public:
## add_mesh_observations: function (data = NULL, group = NULL)
## add_observations: function (data = NULL, edge_number = "edge_number", distance_on_edge = "distance_on_edge",
## build_mesh: function (h = NULL, n = NULL, continuous = TRUE, continuous.outs = FALSE,
## buildC: function (alpha = 2, edge_constraint = FALSE)
## buildDirectionalConstraints: function (alpha = 1)
## C: NULL
## characteristics: list
## check_distance_consistency: function ()
## check_euclidean: function ()
## clear_observations: function ()
## clone: function (deep = FALSE)
## CoB: NULL
## compute_characteristics: function (check_euclidean = FALSE)
## compute_fem: function (petrov = FALSE)
## compute_geodist: function (full = FALSE, obs = TRUE, group = NULL, verbose = 0)
## compute_geodist_mesh: function ()
## compute_geodist_PtE: function (PtE, normalized = TRUE, include_vertices = TRUE, verbose = 0)
## compute_laplacian: function (full = FALSE, obs = TRUE, group = NULL, verbose = 0)
## compute_PtE_edges: function ()
## compute_resdist: function (full = FALSE, obs = TRUE, group = NULL, check_euclidean = FALSE,
## compute_resdist_mesh: function ()
## compute_resdist_PtE: function (PtE, normalized = TRUE, include_vertices = FALSE, check_euclidean = FALSE,
## coordinates: function (PtE = NULL, XY = NULL, normalized = TRUE)
## drop_na: function (...)
## E: 1 3 5 7 9 9 10 12 13 14 15 12 18 19 21 20 22 24 26 28 30 ...
## edge_lengths: 0.0820202978316493 0.13610246403764 0.07378151878521 0.0 ...
## edges: metric_graph_edges
## edgeweight_to_data: function (loc = NULL, mesh = FALSE, data_loc = FALSE, weight_col = NULL,
## fem_basis: function (PtE)
## filter: function (..., .drop_na = FALSE, .drop_all_na = TRUE)
## geo_dist: list
## get_data: function (group = NULL, tibble = TRUE, drop_na = FALSE, drop_all_na = TRUE)
## get_degrees: function (which = "degree")
## get_edge_lengths: function (unit = NULL)
## get_edge_weights: function (data.frame = FALSE, tibble = TRUE)
## get_groups: function (get_cols = FALSE)
## get_initial_graph: function ()
## get_locations: function ()
## get_mesh_locations: function (bru = FALSE, loc = NULL, normalized = TRUE)
## get_PtE: function ()
## get_vertices_incomp_dir: function ()
## initialize: function (edges = NULL, V = NULL, E = NULL, vertex_unit = NULL,
## is_tree: function ()
## Laplacian: NULL
## mesh: list
## mesh_A: function (PtE)
## mutate: function (..., .drop_na = FALSE, .drop_all_na = TRUE)
## nE: 11104
## nV: 8781
## observation_to_vertex: function (tolerance = 1e-15, mesh_warning = TRUE)
## plot: function (data = NULL, newdata = NULL, group = 1, plotly = FALSE,
## plot_connections: function ()
## plot_function: function (data = NULL, newdata = NULL, group = 1, X = NULL, plotly = FALSE,
## plot_movie: function (X, plotly = TRUE, vertex_size = 5, vertex_color = "black",
## print: function ()
## process_data: function (data = NULL, edge_number = "edge_number", distance_on_edge = "distance_on_edge",
## prune_vertices: function (check_weights = TRUE, verbose = FALSE)
## PtV: NULL
## res_dist: NULL
## select: function (..., .drop_na = FALSE, .drop_all_na = TRUE)
## set_edge_weights: function (weights = rep(1, self$nE), kirchhoff_weights = NULL)
## summarise: function (..., .include_graph_groups = FALSE, .groups = NULL,
## summary: function (messages = FALSE, compute_characteristics = TRUE, check_euclidean = TRUE,
## V: -122.40171 -122.40078 -122.44449 -122.44331 -122.41216 - ...
## vertices: metric_graph_vertices
## VtEfirst: function ()
## Private:
## A: function (group = NULL, obs_to_vert = FALSE, drop_na = FALSE,
## add_vertices: function (PtE, tolerance = 1e-10, verbose)
## addinfo: FALSE
## clear_initial_info: function ()
## compute_degrees: function ()
## compute_laplacian_PtE: function (PtE, normalized = TRUE, verbose = verbose)
## compute_lengths: function (longlat, unit, crs, proj4string, which_longlat, vertex_unit,
## connected: TRUE
## coordinates_multiple_snaps: function (XY, tolerance, verbose = verbose, crs, proj4string,
## create_update_vertices: function ()
## crs: crs
## data: metric_graph_data, list
## edge_weights: tbl_df, tbl, data.frame
## find_edge_edge_points: function (tol, verbose, crs, proj4string, longlat, fact, which_longlat)
## find_mesh_bc: function ()
## get_edge_weights_internal: function (data.frame = FALSE)
## group_col: .group
## initial_edges_added: NULL
## initial_graph: metric_graph, R6
## kirchhoff_weights: NULL
## length_unit: km
## line_to_vertex: function (tolerance = 0, longlat = FALSE, fact, verbose, crs,
## longlat: TRUE
## merge_close_vertices: function (tolerance, fact)
## merge.all.deg2: function ()
## mesh_merge_deg2: function ()
## mesh_merge_outs: function ()
## move_V_first: function ()
## plot_2d: function (line_width = 0.1, marker_size = 1, vertex_color = "black",
## plot_3d: function (line_width = 1, marker_size = 1, vertex_color = "rgb(0,0,0)",
## proj4string: NULL
## prune_warning: FALSE
## pruned: FALSE
## PtE_to_mesh: function (PtE)
## ref_edges: 1 5502 2 359 3 4077 4 5117 5 7 5419 8 9 10 11 4817 4613 ...
## remove_circles: function (threshold, verbose, longlat, unit, crs, proj4string,
## remove.first.deg2: function (res)
## set_first_weights: function (weights = rep(1, self$nE))
## set_petrov_matrices: function ()
## split_edge: function (Ei, t, tolerance = 0)
## temp_PtE: NULL
## tolerance: list
## transform: FALSE
## vertex_unit: degrees
## which_longlat: sf
## .. .. .. .. .. .. .. .. .. ..$ fem_mesh :List of 5
## .. .. .. .. .. .. .. .. .. .. ..$ c0:Formal class 'dgTMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. .. .. .. .. .. .. .. ..@ i : int [1:13932] 0 1 2 3 4 5 6 7 8 9 ...
## .. .. .. .. .. .. .. .. .. .. .. .. ..@ j : int [1:13932] 0 1 2 3 4 5 6 7 8 9 ...
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## .. .. .. .. .. .. .. .. .. .. .. .. ..@ factors : list()
## .. .. .. .. .. .. .. .. .. .. ..$ g1:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
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## .. .. .. .. .. .. .. .. .. .. .. .. ..@ p : int [1:13933] 0 4 9 12 15 18 23 26 29 34 ...
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## .. .. .. .. .. .. .. .. .. .. .. .. ..@ factors : list()
## .. .. .. .. .. .. .. .. .. .. ..$ g2:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. .. .. .. .. .. .. .. ..@ i : int [1:81554] 0 1 5399 5681 8781 11463 0 1 4450 8781 ...
## .. .. .. .. .. .. .. .. .. .. .. .. ..@ p : int [1:13933] 0 6 13 18 23 28 37 42 47 56 ...
## .. .. .. .. .. .. .. .. .. .. .. .. ..@ Dim : int [1:2] 13932 13932
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## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. .. .. .. ..@ x : num [1:81554] 1731368 28997 607384 -2117274 -125237 ...
## .. .. .. .. .. .. .. .. .. .. .. .. ..@ factors : list()
## .. .. .. .. .. .. .. .. .. .. ..$ g3:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. .. .. .. .. .. .. .. ..@ i : int [1:124984] 0 1 805 5399 5681 8781 11429 11463 13882 0 ...
## .. .. .. .. .. .. .. .. .. .. .. .. ..@ p : int [1:13933] 0 9 18 25 32 43 56 65 72 85 ...
## .. .. .. .. .. .. .. .. .. .. .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. .. .. .. .. .. .. .. .. .. .. ..@ Dimnames:List of 2
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. .. .. .. ..@ x : num [1:124984] 1.84e+10 1.88e+08 -4.79e+08 9.57e+09 -2.57e+10 ...
## .. .. .. .. .. .. .. .. .. .. .. .. ..@ factors : list()
## .. .. .. .. .. .. .. .. .. .. ..$ g4:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. .. .. .. .. .. .. .. .. .. .. ..@ i : int [1:175232] 0 1 804 805 4450 5399 5681 8781 11429 11463 ...
## .. .. .. .. .. .. .. .. .. .. .. .. ..@ p : int [1:13933] 0 11 23 32 41 58 76 89 98 116 ...
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## .. .. .. .. .. .. .. .. .. .. .. .. ..@ Dimnames:List of 2
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## .. .. .. .. .. .. .. .. .. .. .. .. .. ..$ : NULL
## .. .. .. .. .. .. .. .. .. .. .. .. ..@ x : num [1:175232] 2.12e+14 1.39e+12 8.54e+11 -8.78e+12 1.53e+10 ...
## .. .. .. .. .. .. .. .. .. .. .. .. ..@ factors : list()
## .. .. .. .. .. .. .. .. .. ..$ parameterization : chr "matern"
## .. .. .. .. .. .. .. .. .. ..$ n.spde : int 13932
## .. .. .. .. .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "rspde_metric_graph" "inla_rspde" "inla.cgeneric"
## .. .. .. .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_inla_rspde" "bru_mapper" "list"
## .. .. .. .. .. .. .. ..$ group :List of 1
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## .. .. .. .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_index" "bru_mapper" "list"
## .. .. .. .. .. .. .. ..$ replicate:List of 4
## .. .. .. .. .. .. .. .. ..$ levels : chr [1:4] "1" "2" "3" "4"
## .. .. .. .. .. .. .. .. ..$ factor_mapping: chr "full"
## .. .. .. .. .. .. .. .. ..$ indexed : logi TRUE
## .. .. .. .. .. .. .. .. ..$ n : int 4
## .. .. .. .. .. .. .. .. ..- attr(*, "class")= chr [1:4] "bru_mapper_factor_index" "bru_mapper_factor" "bru_mapper" "list"
## .. .. .. .. .. .. ..$ n_multi :List of 3
## .. .. .. .. .. .. .. ..$ main : num 41796
## .. .. .. .. .. .. .. ..$ group : num 1
## .. .. .. .. .. .. .. ..$ replicate: int 4
## .. .. .. .. .. .. ..$ n_inla_multi :List of 3
## .. .. .. .. .. .. .. ..$ main : num 41796
## .. .. .. .. .. .. .. ..$ group : num 1
## .. .. .. .. .. .. .. ..$ replicate: int 4
## .. .. .. .. .. .. ..$ values_multi :List of 3
## .. .. .. .. .. .. .. ..$ main : int [1:41796] 1 2 3 4 5 6 7 8 9 10 ...
## .. .. .. .. .. .. .. ..$ group : int 1
## .. .. .. .. .. .. .. ..$ replicate: int [1:4] 1 2 3 4
## .. .. .. .. .. .. ..$ values_inla_multi:List of 3
## .. .. .. .. .. .. .. ..$ main : int [1:41796] 1 2 3 4 5 6 7 8 9 10 ...
## .. .. .. .. .. .. .. ..$ group : int 1
## .. .. .. .. .. .. .. ..$ replicate: int [1:4] 1 2 3 4
## .. .. .. .. .. .. ..$ is_linear_multi :List of 3
## .. .. .. .. .. .. .. ..$ main : logi TRUE
## .. .. .. .. .. .. .. ..$ group : logi TRUE
## .. .. .. .. .. .. .. ..$ replicate: logi TRUE
## .. .. .. .. .. .. ..$ n : num 167184
## .. .. .. .. .. .. ..$ n_inla : num 167184
## .. .. .. .. .. .. ..$ is_linear : logi TRUE
## .. .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_multi" "bru_mapper" "list"
## .. .. .. .. .. ..$ scale : list()
## .. .. .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_scale" "bru_mapper" "list"
## .. .. .. .. ..$ : Named logi [1:2] TRUE TRUE
## .. .. .. .. .. ..- attr(*, "names")= chr [1:2] "mapper" "scale"
## .. .. .. .. ..$ is_linear: logi TRUE
## .. .. .. .. ..$ n_multi : Named int [1:2] 167184 NA
## .. .. .. .. .. ..- attr(*, "names")= chr [1:2] "mapper" "scale"
## .. .. .. .. ..$ n : num 167184
## .. .. .. .. ..$ names : chr [1:2] "mapper" "scale"
## .. .. .. .. ..- attr(*, "class")= chr [1:3] "bru_mapper_pipe" "bru_mapper" "list"
## .. .. .. ..- attr(*, "class")= chr [1:2] "component" "list"
## .. .. ..- attr(*, "class")= chr [1:2] "component_list" "list"
## .. .. ..- attr(*, ".Environment")=<environment: R_GlobalEnv>
## .. ..$ formula:Class 'formula' language BRU_response ~ f(Intercept, model = BRU_Intercept_main_model, ngroup = 1, nrep = 1, values = BRU_Intercept_v| __truncated__ ...
## .. .. .. ..- attr(*, ".Environment")=<environment: R_GlobalEnv>
## .. ..- attr(*, "class")= chr [1:2] "bru_model" "list"
## ..$ lhoods :List of 1
## .. ..$ :List of 17
## .. .. ..$ family : chr "T"
## .. .. ..$ formula :Class 'formula' language speed ~ .
## .. .. .. .. ..- attr(*, ".Environment")=<environment: 0x61cb2d2524f8>
## .. .. ..$ response_data :List of 4
## .. .. .. ..$ BRU_response: num [1:25842] 99.8 91.7 99.8 14.5 16.1 ...
## .. .. .. ..$ BRU_E : num 1
## .. .. .. ..$ BRU_Ntrials : num 1
## .. .. .. ..$ BRU_scale : num 1
## .. .. ..$ data :List of 8
## .. .. .. ..$ speed : num [1:25842] 99.8 91.7 99.8 14.5 16.1 ...
## .. .. .. ..$ SpeedLimit : num [1:25842] 4.09 4.09 4.09 -1.04 -1.04 ...
## .. .. .. ..$ .coord_x : num [1:25842] -122 -122 -122 -122 -122 ...
## .. .. .. ..$ .coord_y : num [1:25842] 37.7 37.7 37.7 37.8 37.8 ...
## .. .. .. ..$ .edge_number : num [1:25842] 2 2 2 3 3 3 5 6 6 6 ...
## .. .. .. ..$ .distance_on_edge: num [1:25842] 0.195 0.227 0.363 0.309 0.583 ...
## .. .. .. ..$ .group : chr [1:25842] "1" "1" "1" "1" ...
## .. .. .. ..$ loc : num [1:25842, 1:2] 2 2 2 3 3 3 5 6 6 6 ...
## .. .. .. ..- attr(*, "class")= chr [1:2] "metric_graph_data" "list"
## .. .. ..$ E : num 1
## .. .. ..$ Ntrials : num 1
## .. .. ..$ weights : num 1
## .. .. ..$ scale : num 1
## .. .. ..$ samplers : NULL
## .. .. ..$ linear : logi TRUE
## .. .. ..$ expr : NULL
## .. .. ..$ response : chr "BRU_response"
## .. .. ..$ inla.family : chr "T"
## .. .. ..$ domain : NULL
## .. .. ..$ used :List of 2
## .. .. .. ..$ effect: chr [1:3] "Intercept" "SpeedLimit" "field"
## .. .. .. ..$ latent: chr(0)
## .. .. .. ..- attr(*, "class")= chr "bru_used"
## .. .. ..$ allow_combine : logi TRUE
## .. .. ..$ control.family: NULL
## .. .. ..- attr(*, "class")= chr [1:2] "bru_like" "list"
## .. ..- attr(*, "class")= chr [1:2] "bru_like_list" "list"
## ..$ options :List of 14
## .. ..$ bru_verbose : num 0
## .. ..$ bru_verbose_store: num Inf
## .. ..$ bru_max_iter : num 1
## .. ..$ bru_run : logi TRUE
## .. ..$ bru_int_args :List of 3
## .. .. ..$ method: chr "stable"
## .. .. ..$ nsub1 : num 30
## .. .. ..$ nsub2 : num 9
## .. ..$ bru_method :List of 6
## .. .. ..$ taylor : chr "pandemic"
## .. .. ..$ search : chr "all"
## .. .. ..$ factor : num 1.62
## .. .. ..$ rel_tol : num 0.1
## .. .. ..$ max_step : num 2
## .. .. ..$ line_opt_method: chr "onestep"
## .. ..$ bru_compress_cp : logi TRUE
## .. ..$ bru_debug : logi FALSE
## .. ..$ E : num 1
## .. ..$ Ntrials : num 1
## .. ..$ control.compute :List of 3
## .. .. ..$ config: logi TRUE
## .. .. ..$ dic : logi TRUE
## .. .. ..$ waic : logi TRUE
## .. ..$ control.inla :List of 1
## .. .. ..$ int.strategy: chr "auto"
## .. ..$ control.fixed :List of 1
## .. .. ..$ expand.factor.strategy: chr "inla"
## .. ..$ verbose : logi FALSE
## .. ..- attr(*, "class")= chr [1:2] "bru_options" "list"
## ..$ inlabru_version: Named chr "2.10.1.9007"
## .. ..- attr(*, "names")= chr "version"
## ..$ INLA_version : Named chr "24.05.18-2"
## .. ..- attr(*, "names")= chr "version"
## ..- attr(*, "class")= chr [1:2] "bru_info" "list"
## - attr(*, "class")= chr [1:3] "bru" "iinla" "inla"## Time difference of 49.33176 mins## inlabru version: 2.10.1.9007
## INLA version: 24.05.18-2
## Components:
## Intercept: main = linear(1), group = exchangeable(1L), replicate = iid(1L)
## SpeedLimit: main = linear(SpeedLimit), group = exchangeable(1L), replicate = iid(1L)
## field: main = cgeneric(loc), group = exchangeable(1L), replicate = iid(data_rspde_bru_stat[["repl"]])
## Likelihoods:
## Family: 'T'
## Data class: 'metric_graph_data', 'list'
## Predictor: speed ~ .
## Time used:
## Pre = 0.429, Running = 2704, Post = 10.4, Total = 2714
## Fixed effects:
## mean sd 0.025quant 0.5quant 0.975quant mode kld
## Intercept 23.597 0.092 23.417 23.597 23.777 23.597 0
## SpeedLimit 8.069 0.154 7.767 8.069 8.372 8.069 0
##
## Random effects:
## Name Model
## field CGeneric
##
## Model hyperparameters:
## mean sd 0.025quant 0.5quant
## precision for the student-t observations 0.001 0.00 0.001 0.001
## degrees of freedom for student-t 2.121 0.00 2.121 2.121
## Theta1 for field 3.087 0.00 3.086 3.087
## Theta2 for field -0.002 0.00 -0.002 -0.002
## Theta3 for field -0.888 0.00 -0.888 -0.888
## 0.975quant mode
## precision for the student-t observations 0.001 0.001
## degrees of freedom for student-t 2.121 2.121
## Theta1 for field 3.088 3.087
## Theta2 for field -0.001 -0.002
## Theta3 for field -0.887 -0.888
##
## Deviance Information Criterion (DIC) ...............: 218459.20
## Deviance Information Criterion (DIC, saturated) ....: -7817.43
## Effective number of parameters .....................: 951.04
##
## Watanabe-Akaike information criterion (WAIC) ...: 219620.45
## Effective number of parameters .................: 2088.89
##
## Marginal log-Likelihood: -191633.29
## is computed
## Posterior summaries for the linear predictor and the fitted values are computed
## (Posterior marginals needs also 'control.compute=list(return.marginals.predictor=TRUE)')## mean sd 0.025quant 0.5quant 0.975quant mode
## std.dev 21.910400 9.46258e-03 21.888400 21.912000 21.923900 21.919000
## range 0.998065 2.22487e-04 0.997662 0.998053 0.998559 0.997965
## nu 0.437355 5.47346e-05 0.437212 0.437331 0.437449 0.4373741.2 Nonstationary model
- Observe that we are using the computed parameters from the stationary model as initial values for the nonstationary models.
nonstat.time.ini <- Sys.time()
################################################################################
############################# NON STATIONARY MODEL #############################
################################################################################
B.sigma = cbind(0, 1, 0, mesh$SpeedLimit, 0)
B.range = cbind(0, 0, 1, 0, mesh$SpeedLimit)
init.vec.theta = c(fit.rspde$summary.log.std.dev$mode,
fit.rspde$summary.log.range$mode,
rep(0, (ncol(B.sigma)-3)))
rspde_model_nonstat <- rspde.metric_graph(sf_graph,
start.theta = init.vec.theta,
theta.prior.mean = init.vec.theta,
B.sigma = B.sigma,
B.range = B.range,
parameterization = "matern",
nu.upper.bound = 1.5)str(rspde_model_nonstat)
## List of 20
## $ f :List of 3
## ..$ model : chr "cgeneric"
## ..$ n : int 41796
## ..$ cgeneric:List of 5
## .. ..$ model: chr "inla_cgeneric_rspde_nonstat_general_model"
## .. ..$ shlib: chr "/home/rierasl/R/x86_64-pc-linux-gnu-library/4.4/INLA/bin/linux/64bit/external/rSPDE/librSPDE.so"
## .. ..$ n : int 41796
## .. ..$ debug: logi FALSE
## .. ..$ data :List of 5
## .. .. ..$ ints :List of 6
## .. .. .. ..$ n : int 41796
## .. .. .. ..$ debug : int 0
## .. .. .. ..$ graph_opt_i: int [1:186659] 0 0 0 0 0 0 0 0 0 1 ...
## .. .. .. ..$ graph_opt_j: int [1:186659] 0 1 805 5399 5681 8781 11429 11463 13882 1 ...
## .. .. .. ..$ rspde_order: int 2
## .. .. .. ..$ matern_par : int 1
## .. .. ..$ doubles :List of 9
## .. .. .. ..$ d : num 1
## .. .. .. ..$ nu_upper_bound : num 1.5
## .. .. .. ..$ prior.nu.loglocation: num -0.288
## .. .. .. ..$ prior.nu.logscale : num 1
## .. .. .. ..$ prior.nu.mean : num 0.75
## .. .. .. ..$ prior.nu.prec : num 3
## .. .. .. ..$ start.nu : num 0.75
## .. .. .. ..$ start.theta : num [1:4] 3.08735 -0.00204 0 0
## .. .. .. ..$ theta.prior.mean : num [1:4] 3.08735 -0.00204 0 0
## .. .. ..$ characters:List of 4
## .. .. .. ..$ model : chr "inla_cgeneric_rspde_nonstat_general_model"
## .. .. .. ..$ shlib : chr "/home/rierasl/R/x86_64-pc-linux-gnu-library/4.4/INLA/bin/linux/64bit/external/rSPDE/librSPDE.so"
## .. .. .. ..$ prior.nu.dist : chr "lognormal"
## .. .. .. ..$ prior.theta.param: chr "theta"
## .. .. ..$ matrices :List of 4
## .. .. .. ..$ rational_table : num [1:5996] 999 6 0.001 0.412 0.005 ...
## .. .. .. ..$ B_tau : num [1:69662] 13932 5 -1.15 -1 0.75 ...
## .. .. .. ..$ B_kappa : num [1:69662] 13932 5 0.896 0 -1 ...
## .. .. .. ..$ theta.prior.prec: num [1:18] 4 4 0.1 0 0 0 0 0.1 0 0 ...
## .. .. ..$ smatrices :List of 2
## .. .. .. ..$ C: num [1:41799] 13932 13932 13932 0 1 ...
## .. .. .. ..$ G: num [1:132615] 13932 13932 44204 0 5681 ...
## .. ..- attr(*, "class")= chr "inla.cgeneric"
## $ cgeneric_type : chr "general"
## $ theta.prior.mean : num [1:4] 3.08735 -0.00204 0 0
## $ prior.nu :List of 4
## ..$ loglocation: num -0.288
## ..$ mean : num 0.75
## ..$ prec : num 3
## ..$ logscale : num 1
## $ theta.prior.prec : num [1:4, 1:4] 0.1 0 0 0 0 0.1 0 0 0 0 ...
## $ start.nu : num 0.75
## $ integer.nu : logi FALSE
## $ start.theta : num [1:4] 3.08735 -0.00204 0 0
## $ stationary : logi FALSE
## $ rspde.order : num 2
## $ dim : num 1
## $ est_nu : logi TRUE
## $ nu.upper.bound : num 1.5
## $ prior.nu.dist : chr "lognormal"
## $ debug : logi FALSE
## $ type.rational.approx: chr "chebfun"
## $ mesh :Classes 'metric_graph', 'R6' <metric_graph>
## Public:
## add_mesh_observations: function (data = NULL, group = NULL)
## add_observations: function (data = NULL, edge_number = "edge_number", distance_on_edge = "distance_on_edge",
## build_mesh: function (h = NULL, n = NULL, continuous = TRUE, continuous.outs = FALSE,
## buildC: function (alpha = 2, edge_constraint = FALSE)
## buildDirectionalConstraints: function (alpha = 1)
## C: NULL
## characteristics: list
## check_distance_consistency: function ()
## check_euclidean: function ()
## clear_observations: function ()
## clone: function (deep = FALSE)
## CoB: NULL
## compute_characteristics: function (check_euclidean = FALSE)
## compute_fem: function (petrov = FALSE)
## compute_geodist: function (full = FALSE, obs = TRUE, group = NULL, verbose = 0)
## compute_geodist_mesh: function ()
## compute_geodist_PtE: function (PtE, normalized = TRUE, include_vertices = TRUE, verbose = 0)
## compute_laplacian: function (full = FALSE, obs = TRUE, group = NULL, verbose = 0)
## compute_PtE_edges: function ()
## compute_resdist: function (full = FALSE, obs = TRUE, group = NULL, check_euclidean = FALSE,
## compute_resdist_mesh: function ()
## compute_resdist_PtE: function (PtE, normalized = TRUE, include_vertices = FALSE, check_euclidean = FALSE,
## coordinates: function (PtE = NULL, XY = NULL, normalized = TRUE)
## drop_na: function (...)
## E: 1 3 5 7 9 9 10 12 13 14 15 12 18 19 21 20 22 24 26 28 30 ...
## edge_lengths: 0.0820202978316493 0.13610246403764 0.07378151878521 0.0 ...
## edges: metric_graph_edges
## edgeweight_to_data: function (loc = NULL, mesh = FALSE, data_loc = FALSE, weight_col = NULL,
## fem_basis: function (PtE)
## filter: function (..., .drop_na = FALSE, .drop_all_na = TRUE)
## geo_dist: list
## get_data: function (group = NULL, tibble = TRUE, drop_na = FALSE, drop_all_na = TRUE)
## get_degrees: function (which = "degree")
## get_edge_lengths: function (unit = NULL)
## get_edge_weights: function (data.frame = FALSE, tibble = TRUE)
## get_groups: function (get_cols = FALSE)
## get_initial_graph: function ()
## get_locations: function ()
## get_mesh_locations: function (bru = FALSE, loc = NULL, normalized = TRUE)
## get_PtE: function ()
## get_vertices_incomp_dir: function ()
## initialize: function (edges = NULL, V = NULL, E = NULL, vertex_unit = NULL,
## is_tree: function ()
## Laplacian: NULL
## mesh: list
## mesh_A: function (PtE)
## mutate: function (..., .drop_na = FALSE, .drop_all_na = TRUE)
## nE: 11104
## nV: 8781
## observation_to_vertex: function (tolerance = 1e-15, mesh_warning = TRUE)
## plot: function (data = NULL, newdata = NULL, group = 1, plotly = FALSE,
## plot_connections: function ()
## plot_function: function (data = NULL, newdata = NULL, group = 1, X = NULL, plotly = FALSE,
## plot_movie: function (X, plotly = TRUE, vertex_size = 5, vertex_color = "black",
## print: function ()
## process_data: function (data = NULL, edge_number = "edge_number", distance_on_edge = "distance_on_edge",
## prune_vertices: function (check_weights = TRUE, verbose = FALSE)
## PtV: NULL
## res_dist: NULL
## select: function (..., .drop_na = FALSE, .drop_all_na = TRUE)
## set_edge_weights: function (weights = rep(1, self$nE), kirchhoff_weights = NULL)
## summarise: function (..., .include_graph_groups = FALSE, .groups = NULL,
## summary: function (messages = FALSE, compute_characteristics = TRUE, check_euclidean = TRUE,
## V: -122.40171 -122.40078 -122.44449 -122.44331 -122.41216 - ...
## vertices: metric_graph_vertices
## VtEfirst: function ()
## Private:
## A: function (group = NULL, obs_to_vert = FALSE, drop_na = FALSE,
## add_vertices: function (PtE, tolerance = 1e-10, verbose)
## addinfo: FALSE
## clear_initial_info: function ()
## compute_degrees: function ()
## compute_laplacian_PtE: function (PtE, normalized = TRUE, verbose = verbose)
## compute_lengths: function (longlat, unit, crs, proj4string, which_longlat, vertex_unit,
## connected: TRUE
## coordinates_multiple_snaps: function (XY, tolerance, verbose = verbose, crs, proj4string,
## create_update_vertices: function ()
## crs: crs
## data: metric_graph_data, list
## edge_weights: tbl_df, tbl, data.frame
## find_edge_edge_points: function (tol, verbose, crs, proj4string, longlat, fact, which_longlat)
## find_mesh_bc: function ()
## get_edge_weights_internal: function (data.frame = FALSE)
## group_col: .group
## initial_edges_added: NULL
## initial_graph: metric_graph, R6
## kirchhoff_weights: NULL
## length_unit: km
## line_to_vertex: function (tolerance = 0, longlat = FALSE, fact, verbose, crs,
## longlat: TRUE
## merge_close_vertices: function (tolerance, fact)
## merge.all.deg2: function ()
## mesh_merge_deg2: function ()
## mesh_merge_outs: function ()
## move_V_first: function ()
## plot_2d: function (line_width = 0.1, marker_size = 1, vertex_color = "black",
## plot_3d: function (line_width = 1, marker_size = 1, vertex_color = "rgb(0,0,0)",
## proj4string: NULL
## prune_warning: FALSE
## pruned: FALSE
## PtE_to_mesh: function (PtE)
## ref_edges: 1 5502 2 359 3 4077 4 5117 5 7 5419 8 9 10 11 4817 4613 ...
## remove_circles: function (threshold, verbose, longlat, unit, crs, proj4string,
## remove.first.deg2: function (res)
## set_first_weights: function (weights = rep(1, self$nE))
## set_petrov_matrices: function ()
## split_edge: function (Ei, t, tolerance = 0)
## temp_PtE: NULL
## tolerance: list
## transform: FALSE
## vertex_unit: degrees
## which_longlat: sf
## $ fem_mesh :List of 5
## ..$ c0:Formal class 'dgTMatrix' [package "Matrix"] with 6 slots
## .. .. ..@ i : int [1:13932] 0 1 2 3 4 5 6 7 8 9 ...
## .. .. ..@ j : int [1:13932] 0 1 2 3 4 5 6 7 8 9 ...
## .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. ..@ Dimnames:List of 2
## .. .. .. ..$ : NULL
## .. .. .. ..$ : NULL
## .. .. ..@ x : num [1:13932] 0.0534 0.0776 0.0408 0.0457 0.0367 ...
## .. .. ..@ factors : list()
## ..$ g1:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. ..@ i : int [1:44204] 0 5681 8781 11463 1 8781 11429 11463 13882 2 ...
## .. .. ..@ p : int [1:13933] 0 4 9 12 15 18 23 26 29 34 ...
## .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. ..@ Dimnames:List of 2
## .. .. .. ..$ : NULL
## .. .. .. ..$ : NULL
## .. .. ..@ x : num [1:44204] 210.6 -161.9 -24.4 -24.4 103.4 ...
## .. .. ..@ factors : list()
## ..$ g2:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. ..@ i : int [1:81554] 0 1 5399 5681 8781 11463 0 1 4450 8781 ...
## .. .. ..@ p : int [1:13933] 0 6 13 18 23 28 37 42 47 56 ...
## .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. ..@ Dimnames:List of 2
## .. .. .. ..$ : NULL
## .. .. .. ..$ : NULL
## .. .. ..@ x : num [1:81554] 1731368 28997 607384 -2117274 -125237 ...
## .. .. ..@ factors : list()
## ..$ g3:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. ..@ i : int [1:124984] 0 1 805 5399 5681 8781 11429 11463 13882 0 ...
## .. .. ..@ p : int [1:13933] 0 9 18 25 32 43 56 65 72 85 ...
## .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. ..@ Dimnames:List of 2
## .. .. .. ..$ : NULL
## .. .. .. ..$ : NULL
## .. .. ..@ x : num [1:124984] 1.84e+10 1.88e+08 -4.79e+08 9.57e+09 -2.57e+10 ...
## .. .. ..@ factors : list()
## ..$ g4:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. .. ..@ i : int [1:175232] 0 1 804 805 4450 5399 5681 8781 11429 11463 ...
## .. .. ..@ p : int [1:13933] 0 11 23 32 41 58 76 89 98 116 ...
## .. .. ..@ Dim : int [1:2] 13932 13932
## .. .. ..@ Dimnames:List of 2
## .. .. .. ..$ : NULL
## .. .. .. ..$ : NULL
## .. .. ..@ x : num [1:175232] 2.12e+14 1.39e+12 8.54e+11 -8.78e+12 1.53e+10 ...
## .. .. ..@ factors : list()
## $ parameterization : chr "matern"
## $ n.spde : int 13932
## - attr(*, "class")= chr [1:3] "rspde_metric_graph" "inla_rspde" "inla.cgeneric"str(data_rspde_bru_nonstat)
## List of 4
## $ data :List of 8
## ..$ speed : num [1:25842] 99.8 91.7 99.8 14.5 16.1 ...
## ..$ SpeedLimit : num [1:25842] 4.09 4.09 4.09 -1.04 -1.04 ...
## ..$ .coord_x : num [1:25842] -122 -122 -122 -122 -122 ...
## ..$ .coord_y : num [1:25842] 37.7 37.7 37.7 37.8 37.8 ...
## ..$ .edge_number : num [1:25842] 2 2 2 3 3 3 5 6 6 6 ...
## ..$ .distance_on_edge: num [1:25842] 0.195 0.227 0.363 0.309 0.583 ...
## ..$ .group : chr [1:25842] "1" "1" "1" "1" ...
## ..$ loc : num [1:25842, 1:2] 2 2 2 3 3 3 5 6 6 6 ...
## ..- attr(*, "class")= chr [1:2] "metric_graph_data" "list"
## $ index:List of 3
## ..$ field : int [1:55728] 1 2 3 4 5 6 7 8 9 10 ...
## ..$ field.group: int [1:55728] 1 1 1 1 1 1 1 1 1 1 ...
## ..$ field.repl : int [1:55728] 1 1 1 1 1 1 1 1 1 1 ...
## ..- attr(*, "class")= chr [1:2] "inla_rspde_index" "list"
## ..- attr(*, "rspde.order")= num 0
## ..- attr(*, "integer_nu")= logi TRUE
## ..- attr(*, "n.mesh")= int 13932
## ..- attr(*, "name")= chr "field"
## ..- attr(*, "n.group")= int 1
## ..- attr(*, "n.repl")= int 4
## $ repl : chr [1:25842] "1" "1" "1" "1" ...
## $ basis:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
## .. ..@ i : int [1:155052] 0 1 3 8 9 10 11 12 13 14 ...
## .. ..@ p : int [1:167185] 0 0 0 2 2 10 16 16 16 21 ...
## .. ..@ Dim : int [1:2] 25842 167184
## .. ..@ Dimnames:List of 2
## .. .. ..$ : NULL
## .. .. ..$ : NULL
## .. ..@ x : num [1:155052] 0.416 0.319 0.382 0.224 0.509 ...
## .. ..@ factors : list()cmp_nonstat = speed ~ -1 +
Intercept(1) +
SpeedLimit +
field(loc, model = rspde_model_nonstat,
replicate = data_rspde_bru_nonstat[["repl"]])
rspde_fit_nonstat <-
bru(cmp_nonstat,
data = data_rspde_bru_nonstat[["data"]],
family = "T",
options = list(verbose = FALSE)
)
##
## *** inla.core.safe: The inla program failed, but will rerun in case better initial values may help. try=1/1
##
## *** inla.core.safe: rerun with improved initial values## Time difference of 2.870091 hours## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'summary': object 'rspde_fit_nonstat' not found## Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'summary': object 'rspde_fit_nonstat' not found1.3 Crossvalidation 1
#load(here("Models_output/distmatrixfixed.RData"))
points = data %>%
as.data.frame() %>%
st_as_sf(coords = c(".coord_x", ".coord_y"), crs = 4326) %>%
mutate(., index = 1:nrow(.)) %>%
st_drop_geometry() %>%
dplyr:::select(speed, .group, index) %>%
mutate(.group = as.numeric(.group)) %>%
group_by(.group) %>%
mutate(indexingroup = seq_len(n())) %>%
ungroup()
distance = seq(from = 0, to = 200, by = 20)/1000The code of chunk below was executed only one time.
{r}
load(here("Models_output/distmatrixfixed_19May24.RData"))
points = data %>%
as.data.frame() %>%
st_as_sf(coords = c(".coord_x", ".coord_y"), crs = 4326) %>%
mutate(., index = 1:nrow(.)) %>%
st_drop_geometry() %>%
dplyr:::select(speed, .group, index) %>%
mutate(.group = as.numeric(.group)) %>%
group_by(.group) %>%
mutate(indexingroup = seq_len(n())) %>%
ungroup()
distance = seq(from = 0, to = 200, by = 20)/1000
GROUPS <- list()
for (j in 1:length(distance)) {
print(j)
GROUPS[[j]] = list()
for (i in 1:nrow(points)) {
rowi = points[i, ]
GROUPS[[j]][[i]] <- which(as.vector(distmatrixlist[[rowi$.group]][rowi$indexingroup,]) <= distance[j])
}
}
save(GROUPS, file = here("Models_output/GROUPS_19May24.RData"))The code of chunk above was executed only one time.
load(here("Models_output/GROUPS_19May24.RData"))
mse.stat <- mse.nonstat <- ls.stat <- ls.nonstat <- rep(0,length(distance))
# cross-validation for-loop
for (j in 1:length(distance)) {
print(j)
# cross-validation of the stationary model
cv.stat <- inla.group.cv(rspde_fit_stat, groups = GROUPS[[j]])
# cross-validation of the nonstationary model
cv.nonstat <- inla.group.cv(rspde_fit_nonstat, groups = GROUPS[[j]])
# obtain MSE and LS
mse.stat[j] <- mean((cv.stat$mean - points$speed)^2)
mse.nonstat[j] <- mean((cv.nonstat$mean - points$speed)^2)
ls.stat[j] <- mean(log(cv.stat$cv))
ls.nonstat[j] <- mean(log(cv.nonstat$cv))
}
## [1] 1
## Error in eval(expr, envir, enclos): object 'rspde_fit_nonstat' not found
## plot results
par(mfrow = c(2,2), family = "Palatino")
# Plot MSE
plot(distance, mse.stat, main = "MSE", ylim = c(min(mse.nonstat, mse.stat), max(mse.nonstat, mse.stat)),
type = "l", ylab = "MSE", xlab = "distance in m", col = "black")
lines(distance, mse.nonstat, col = "blue")
legend("bottomright", legend = c("Stationary", "Non-stationary"), col = c("black", "blue"), lty = 1)
# Plot log-score
plot(distance, -ls.stat, main = "log-score", ylim = c(min(-ls.nonstat, -ls.stat), max(-ls.nonstat, -ls.stat)),
type = "l", ylab = "log-score", xlab = "distance in m", col = "black")
lines(distance, -ls.nonstat, col = "blue")
legend("bottomright", legend = c("Stationary", "Non-stationary"), col = c("black", "blue"), lty = 1)